Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/spades/spades_3.13.1+dfsg-2+b2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/spades-3.13.1+dfsg-2+b2k533iexg/spades_3.13.1+dfsg-2+b2_amd64.buildinfo Get source package info: spades=3.13.1+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/spades/3.13.1+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=asciidoctor=2.0.10-2 autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-3 binutils-common=2.35.1-3 binutils-x86-64-linux-gnu=2.35.1-3 bsdextrautils=2.36.1-1 bsdutils=1:2.36.1-1 build-essential=12.8 bwa=0.7.17-5 bzip2=1.0.8-4 ca-certificates=20200601 cmake=3.18.4-1 cmake-data=3.18.4-1 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-17 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-17 gcc=4:10.2.0-1 gcc-10=10.2.0-17 gcc-10-base=10.2.0-17 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.0-17 libatomic1=10.2.0-17 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbam-dev=0.1.19+dfsg-1 libbamtools-dev=2.5.1+dfsg-7 libbamtools2.5.1=2.5.1+dfsg-7 libbinutils=2.35.1-3 libblkid1=2.36.1-1 libboost-dev=1.71.0.3 libboost1.71-dev=1.71.0-7+b1 libbrotli1=1.0.9-2+b1 libbsd0=0.10.0-1 libbwa-dev=0.7.17-5 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-17 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-3 libctf0=2.35.1-3 libcurl3-gnutls=7.72.0-1 libcurl4=7.72.0-1 libcurl4-gnutls-dev=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdeflate-dev=1.6-1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-17 libgcc-s1=10.2.0-17 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.6.15-4 libgomp1=10.2.0-17 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhat-trie-dev=0.1.2-2 libhat-trie0=0.1.2-2 libhogweed6=3.6-2 libhts-dev=1.11-2 libhts3=1.11-2 libicu67=67.1-4 libidn11=1.33-2.4 libidn2-0=2.3.0-4 libisl22=0.22.1-1 libitm1=10.2.0-17 libjsoncpp1=1.7.4-3.1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.0-17 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36.1-1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20200918-1 libncursesw6=6.2+20200918-1 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libnlopt-cxx-dev=2.6.1-8+b2 libnlopt-cxx0=2.6.1-8+b2 libnlopt-dev=2.6.1-8+b2 libnlopt0=2.6.1-8+b2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libprocps8=2:3.3.16-5 libpsl5=0.21.0-1.1 libpython3-dev=3.9.0-3 libpython3-stdlib=3.9.0-3 libpython3.9=3.9.0-5 libpython3.9-dev=3.9.0-5 libpython3.9-minimal=3.9.0-5 libpython3.9-stdlib=3.9.0-5 libquadmath0=10.2.0-17 libreadline8=8.1~rc2-2 librhash0=1.4.0-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libruby2.7=2.7.2-3 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-1 libsqlite3-0=3.33.0-1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1h-1 libssw-dev=1.1-11+b1 libssw0=1.1-11+b1 libstdc++-10-dev=10.2.0-17 libstdc++6=10.2.0-17 libsub-override-perl=0.09-2 libsystemd0=246.6-3 libtasn1-6=4.16.0-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-17 libubsan1=10.2.0-17 libuchardet0=0.0.7-1 libudev1=246.6-3 libunistring2=0.9.10-4 libuuid1=2.36.1-1 libuv1=1.40.0-1 libxml2=2.9.10+dfsg-6.2 libyaml-0-2=0.2.2-1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 lynx=2.9.0dev.6-1 lynx-common=2.9.0dev.6-1 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 mime-support=3.66 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 openssl=1.1.1h-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 procps=2:3.3.16-5 python3=3.9.0-3 python3-dev=3.9.0-3 python3-distutils=3.8.6-1 python3-joblib=0.17.0-0.1 python3-lib2to3=3.8.6-1 python3-minimal=3.9.0-3 python3-pkg-resources=50.3.0-1 python3-yaml=5.3.1-3 python3.9=3.9.0-5 python3.9-dev=3.9.0-5 python3.9-minimal=3.9.0-5 rake=13.0.1-4 readline-common=8.1~rc2-2 ruby=1:2.7+2 ruby-asciidoctor=2.0.10-2 ruby-minitest=5.13.0-1 ruby-net-telnet=0.1.1-2 ruby-power-assert=1.1.7-1 ruby-rubygems=3.2.0~rc.2-2 ruby-test-unit=3.3.5-1 ruby-xmlrpc=0.3.0-2 ruby2.7=2.7.2-3 rubygems-integration=1.17.2 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36.1-1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d spades=3.13.1+dfsg-2 && mkdir -p /build/spades-lv6OTz && dpkg-source --no-check -x /*.dsc /build/spades-lv6OTz/spades-3.13.1+dfsg && cd /build/spades-lv6OTz/spades-3.13.1+dfsg && { printf '%s' 'spades (3.13.1+dfsg-2+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Python 3.9 as default -- amd64 / i386 Build Daemon (x86-csail-01) Thu, 19 Nov 2020 01:35:41 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/spades-lv6OTz" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/spades-lv6OTz/spades-3.13.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605749741" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/spades-lv6OTz /tmp/spades-3.13.1+dfsg-2+b2k533iexg bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.FGYy2dUtLp as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.FGYy2dUtLp Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (748 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4690 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.FGYy2dUtLp Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 22s (1017 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.FGYy2dUtLp I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d spades=3.13.1+dfsg-2 && mkdir -p /build/spades-lv6OTz && dpkg-source --no-check -x /*.dsc /build/spades-lv6OTz/spades-3.13.1+dfsg && cd /build/spades-lv6OTz/spades-3.13.1+dfsg && { printf '%s' 'spades (3.13.1+dfsg-2+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Python 3.9 as default -- amd64 / i386 Build Daemon (x86-csail-01) Thu, 19 Nov 2020 01:35:41 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/spades-lv6OTz"' exec /tmp/mmdebstrap.FGYy2dUtLp Reading package lists... NOTICE: 'spades' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/spades.git Please use: git clone https://salsa.debian.org/med-team/spades.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3230 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main spades 3.13.1+dfsg-2 (dsc) [2381 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main spades 3.13.1+dfsg-2 (tar) [3203 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main spades 3.13.1+dfsg-2 (diff) [25.2 kB] Fetched 3230 kB in 3s (1229 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'spades_3.13.1+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting spades in /build/spades-lv6OTz/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: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/spades-lv6OTz/spades-3.13.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605749741" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.FGYy2dUtLp dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.13.1+dfsg-2+b2 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) 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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/debian/man_src/*.html /build/spades-lv6OTz/spades-3.13.1+dfsg/debian/man_src/*.? rm -rf /build/spades-lv6OTz/spades-3.13.1+dfsg/debian/man make[1]: Leaving directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg' dh_clean -X.orig make[1]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' debian/rules build-arch dh build-arch --with python3 --sourcedirectory=assembler/src --buildsystem=cmake dh_update_autotools_config -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_autoreconf -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' cd assembler && PREFIX=/build/spades-lv6OTz/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 10.2.0 -- The CXX compiler identification is GNU 10.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done 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-1.71.0/BoostConfig.cmake (found version "1.71.0") 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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades make[2]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' /usr/bin/cmake -S/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -B/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/CMakeFiles /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/arena.c.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c: In function 'malloc_vsnprintf': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cmake -P CMakeFiles/jemalloc.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 9%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/Matrix/DenseMatrix.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/Matrix/SparseMatrix.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/Poa/PoaConfig.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp [ 14%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/Poa/PoaConsensus.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp [ 14%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/Poa/PoaGraph.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp [ 14%] Linking CXX static library libConsensusCore.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 /usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o /usr/bin/ranlib libConsensusCore.a make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 14%] Built target ConsensusCore make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api/CMakeFiles/BamTools.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api/CMakeFiles/BamTools.dir/depend.internal". Scanning dependencies of target BamTools make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 14%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/BamAlignment.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/BamAlignment.cpp [ 14%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/BamMultiReader.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp [ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/BamReader.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/BamReader.cpp [ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/BamWriter.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/BamWriter.cpp [ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SamHeader.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SamProgram.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/SamProgram.cpp [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SamProgramChain.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SamReadGroup.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/SamReadGroup.cpp [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SamReadGroupDictionary.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SamSequence.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SamSequenceDictionary.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/SamSequenceDictionary.cpp [ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/bam/BamHeader_p.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp [ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/bam/BamMultiReader_p.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp [ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/bam/BamRandomAccessController_p.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/bam/BamReader_p.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/bam/BamWriter_p.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: At top level: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 /usr/bin/ar qc libBamTools.a CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o /usr/bin/ranlib libBamTools.a make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 30%] Built target BamTools make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools/CMakeFiles/samtools.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools/CMakeFiles/samtools.dir/depend.internal". Scanning dependencies of target samtools make[4]: Leaving directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 30%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/kstring.c.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/kstring.c [ 32%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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_aux.c.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_aux.c [ 32%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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.c.o -c /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_core': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function '_razf_write': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_close': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_end_flush': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'save_zindex': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_cat.c [ 38%] Linking CXX static library libsamtools.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/cppformat /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/format.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 38%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/cppformat -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/cppformat -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/cppformat/posix.cc [ 39%] Linking CXX static library libformat.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/cityhash /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 39%] Building CXX object ext/cityhash/CMakeFiles/cityhash.dir/city.cc.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/cityhash -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/cityhash/city.cc [ 40%] Linking CXX static library libcityhash.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash && /usr/bin/cmake -P CMakeFiles/cityhash.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/getopt_pp /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/getopt_pp -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/getopt_pp/getopt_pp.cpp [ 41%] Linking CXX static library libgetopt_pp.a cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/Signals.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm/Signals.cpp [ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/SmallVector.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm/SmallVector.cpp [ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/regerror.c.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm/regerror.c [ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o cd /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/regexec.c.o -c /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/llvm/regstrlcpy.c [ 51%] Linking CXX static library libllvm-support.a cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gqf /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/gqf.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 52%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gqf -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_init': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/gqf/gqf.h: In function 'qf_deserialize': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/edlib /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/edlib.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/edlib -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/edlib/edlib.cpp [ 53%] Linking CXX static library libedlib.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gfa1 /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gfa1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/src/gfa1/gfa.c [ 53%] Linking C static library libgfa1.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/input.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 54%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/sam/sam_reader.cpp [ 55%] Linking CXX static library libinput.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 57%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:34:44: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:24:50: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:24:50: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:24:50: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:34:44: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/library.cpp [ 58%] Linking CXX static library libpipeline.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/sequence /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence/CMakeFiles/sequence.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence/CMakeFiles/sequence.dir/depend.internal". Scanning dependencies of target sequence make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 58%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/sequence -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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/sequence.dir/sequence_tools.cpp.o -c /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence_tools.cpp [ 59%] Linking CXX static library libsequence.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 /usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o /usr/bin/ranlib libsequence.a make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 59%] Built target sequence make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/depend.internal". Scanning dependencies of target assembly_graph make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 60%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/reads/header_naming.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/utils/edge_namer.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:54:1: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:54:1: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:54:1: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/modules.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/modules.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:442:63: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:497:60: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:400:57: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:497:60: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:497:60: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:442:63: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/stl_utils.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/paired_info.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/stages.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/stages.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 71%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:231:82: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:198:73: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:198:73: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:198:73: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:33, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:3, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:255:113: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:138, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/parallel_simplification_algorithms.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/parallel_simplification_algorithms.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:28, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:73:43: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/utils.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/utils.dir/depend.internal". Scanning dependencies of target utils make[4]: Leaving directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 73%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger_impl.cpp [ 76%] Linking CXX static library libutils.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/1.cpp [ 76%] Linking CXX static library libmph_index.a cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/common_modules.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/common_modules.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/common_modules.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Building CXX object common/CMakeFiles/common_modules.dir/empty.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/empty.cpp [ 76%] Linking CXX static library libcommon_modules.a cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/graph /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/graphio.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/graph -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/graph/fastg_writer.cpp [ 77%] Linking CXX static library libgraphio.a cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-stages.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:26:60: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:15: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:28, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:73:43: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:319:109: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:135, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_filler.hpp:75:39: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:9, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:206:77: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:112:53: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:112:53: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:118:53: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:206:77: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:206:77: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/stl_utils.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-core.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 80%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/filesystem/path_helper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:214:25: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:214:25: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 82%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_data.cpp:102:22: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_data.cpp:102:22: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_data.cpp:102:22: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/hammer/expander.cpp [ 85%] Linking CXX executable ../../bin/spades-hammer cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:8, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:80:22: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:80:22: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:80:22: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/penalty_estimator.hpp:43, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:26: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/penalty_estimator.hpp:44, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:26: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:26: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:28: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:18, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.h:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.h:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp:5: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector/contig_processor.cpp /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/corrector/main.cpp [ 94%] Linking CXX executable ../../bin/spades-corrector-core cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/filesystem/path_helper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount/read_filter.cpp [ 96%] Linking CXX executable ../../bin/spades-read-filter cd /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 97%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:99:32: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:99:32: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:99:32: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 98%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:231:82: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:151:121: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:151:121: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:151:121: required from here /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake --color= Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake" is newer than depender "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/depend.internal". Dependee "/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 98%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o cd /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src -I/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp In file included from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [100%] Built target spades-gmapper make[3]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' /usr/bin/cmake -E cmake_progress_start /build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades/CMakeFiles 0 make[2]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[2]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[3]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 9%] Built target jemalloc make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 14%] Built target ConsensusCore make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 30%] Built target BamTools make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 38%] Built target samtools make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 39%] Built target format make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 40%] Built target cityhash make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 41%] Built target getopt_pp make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 51%] Built target llvm-support make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 52%] Built target gqf make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Built target edlib make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Built target gfa1 make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 54%] Built target coverage_model make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 55%] Built target input make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 58%] Built target pipeline make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 59%] Built target sequence make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 63%] Built target assembly_graph make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 67%] Built target path_extend make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 70%] Built target modules make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 71%] Built target paired_info make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 72%] Built target stages make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target utils make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target mph_index make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target common_modules make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 77%] Built target graphio make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 80%] Built target spades-stages make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 82%] Built target spades-core make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 85%] Built target spades-hammer make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 91%] Built target spades-ionhammer make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 94%] Built target spades-corrector-core make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 95%] Built target spades-truseq-scfcorrection make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 96%] Built target spades-read-filter make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 97%] Built target spades-kmercount make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [ 98%] Built target spades-gbuilder make[4]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' [100%] Built target spades-gmapper make[3]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' Install the project... -- Install configuration: "RelWithDebInfo" -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/metaspades.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/plasmidspades.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/rnaspades.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/truspades.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades_init.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/VERSION -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.gff -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.gff -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.txt -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.txt -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R1.fastq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/manual.html -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/README.md -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/truspades_manual.html -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/rnaspades_manual.html -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/LICENSE -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/GPLv2.txt -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-core -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/toy.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/config.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/moleculo_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/construction.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/tsa.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/simplification.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mode.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/pe_params.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-hammer -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/hammer -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/hammer/config.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-ionhammer -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/ionhammer -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/ionhammer/ionhammer.cfg -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-corrector-core -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/corrector -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/corrector/corrector.info -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-truseq-scfcorrection -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-kmercount -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-gbuilder -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-gmapper -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/hammer_logic.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/spades_logic.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/corrector_logic.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/support.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/options_storage.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/lucigen_nxmate.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/reference_construction.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/break_by_coverage.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/barcode_extraction.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/generate_quality.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/id_generation.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/launch_options.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/string_dist_utils.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/alignment.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/parallel_launcher.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/sam_parser.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/SeqIO.py -- Installing: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/__init__.py make[2]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg/assembler/build_spades' find /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades \ -type f \ -print0 \ -exec sed -i 's/pyyaml[2|3]/yaml/' {} + /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades_init.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-truseq-scfcorrection/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-kmercount/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-corrector-core/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/truspades.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-gbuilder/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-gmapper/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-core/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-hammer/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-ionhammer/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/GPLv2.txt/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/corrector/corrector.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/toy.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/config.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/moleculo_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/construction.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/distance_estimation.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/mda_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/tsa.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/detail_info_printer.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/rna_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mda_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/plasmid_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/large_genome_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/meta_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/simplification.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mode.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/pe_params.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/ionhammer/ionhammer.cfg/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/configs/hammer/config.info/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R2.fastq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R2.fastq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R1.fastq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R1.fastq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/lucigen_nxmate.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/launch_options.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/barcode_extraction.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/generate_quality.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/id_generation.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/string_dist_utils.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/reference_construction.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/break_by_coverage.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/spades_logic.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/options_storage.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/process_cfg.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/hammer_logic.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/corrector_logic.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/sam_parser.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/__init__.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/alignment.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/SeqIO.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/parallel_launcher.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/support.py/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.gff/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.gff/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/reference_1K.fa.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.txt/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.txt/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/manual.html/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/rnaspades_manual.html/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/VERSION/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl1.fq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl2.fq.gz/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/truspades_manual.html/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/LICENSE/build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades/README.mdmake[1]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' # Ugly hack to make files available for dh_aut_test and autopkgtest mkdir -p /build/spades-lv6OTz/spades-3.13.1+dfsg/../share/ ln -s /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/share/spades /build/spades-lv6OTz/spades-3.13.1+dfsg/../share/ ln -s /usr/bin/bwa /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-bwa /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades.py --test Command line: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades.py --test System information: SPAdes version: 3.13.1 Python version: 3.9.0 OS: Linux-5.10.0-8-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-lv6OTz/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/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/tmp Threads: 16 Memory limit (in Gb): 125 ======= SPAdes pipeline started. Log can be found here: /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/spades.log ===== Read error correction started. == Running read error correction tool: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-hammer /build/spades-lv6OTz/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-lv6OTz/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 125 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. 0:00:00.002 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: 2.60409 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:02.057 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:02.769 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:03.242 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed 0:00:03.790 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.158 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. 0:00:04.159 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.233 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:04.434 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:04.449 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). 0:00:04.450 64M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:00:04.549 64M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. 0:00:04.746 64M / 8G INFO General (main.cpp : 155) Extracting clusters 0:00:04.937 64M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 0:00:04.937 64M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:00:04.937 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:05.258 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:05.662 64M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:00:05.662 64M / 8G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. 0:00:05.664 64M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph 0:00:05.758 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. 0:00:05.758 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 0:00:05.759 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good 0:00:05.759 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good 0:00:05.759 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good 0:00:05.759 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers 0:00:05.759 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 0:00:05.759 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 0:00:05.759 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)) 0:00:05.760 64M / 8G INFO General (main.cpp : 178) Finished clustering. 0:00:05.760 64M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. 0:00:06.042 64M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. 0:00:06.042 64M / 8G INFO General (main.cpp : 222) Solid k-mers finalized 0:00:06.043 64M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. 0:00:06.043 64M / 8G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:06.351 408M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. 0:00:06.534 408M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:00:06.556 408M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 0:00:06.663 64M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. 0:00:06.663 64M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. 0:00:06.663 64M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml 0:00:06.663 64M / 8G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 125 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-lv6OTz/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 0:00:00.000 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 : 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 0:00:00.141 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written 0:00:00.143 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads 0:00:00.299 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.300 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:00.435 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.437 4M / 140M INFO General (construction.cpp : 111) Max read length 100 0:00:00.437 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.437 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.437 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.438 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.438 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60409 Gb 0:00:00.438 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:03.085 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:03.530 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:03.530 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:03.894 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. 0:00:03.894 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.003 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.004 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.004 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.004 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.004 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:04.004 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:08.008 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. 0:00:08.809 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.116 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. 0:00:09.117 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.211 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:09.409 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:09.485 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). 0:00:09.485 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:09.580 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:09.581 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:09.581 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:09.581 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:09.698 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper 0:00:09.698 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:09.699 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:09.794 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:09.900 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:09.986 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.106 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.106 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.106 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.413 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). 0:00:10.413 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:10.587 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:10.680 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:10.680 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 0:00:10.680 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 348 0:00:10.680 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 348. Coverage mad: 62.2692 0:00:10.680 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:10.872 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:11.115 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:11.541 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:12.140 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:13.298 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:00:16.089 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 342.845. Fitted coverage std. dev: 68.3997 0:00:16.091 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999994 0:00:16.091 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 355 0:00:16.091 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 171 0:00:16.091 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 749 0:00:16.091 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 342.845 0:00:16.092 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 171 0:00:16.092 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:16.092 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:16.092 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:16.092 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:16.093 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:16.103 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:16.103 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:16.194 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:16.194 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:16.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:16.281 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:16.383 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:16.383 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:16.383 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:16.383 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:16.383 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:16.384 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.471 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.471 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.496 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.496 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.610 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.614 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.614 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.614 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.614 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.614 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.614 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.615 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.615 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.615 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.615 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.615 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:16.615 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.699 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.699 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.876 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.876 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.898 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.898 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:16.898 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:16.898 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:16.898 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:16.898 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:16.898 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.994 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.994 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.102 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.102 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.182 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.182 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.274 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.274 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:17.275 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:17.305 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:17.306 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:17.306 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 0:00:17.306 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:17.306 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta 0:00:17.307 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:17.307 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-lv6OTz/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 125 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-lv6OTz/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. 0:00:00.002 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: 2.60409 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.978 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:05.060 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:05.060 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.452 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. 0:00:05.452 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.486 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.486 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.486 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.486 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.486 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:05.486 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:08.370 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. 0:00:08.910 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.189 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. 0:00:09.189 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.290 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:09.481 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:09.483 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). 0:00:09.483 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:09.562 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:09.562 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:09.562 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:09.562 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:09.743 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper 0:00:09.744 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:09.744 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:09.843 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:09.878 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:09.958 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.170 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.170 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.171 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.465 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). 0:00:10.465 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:10.654 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:10.754 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:10.754 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 0:00:10.754 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 17 0:00:10.754 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 17. Coverage mad: 11.8608 0:00:10.754 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:10.802 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:10.913 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:11.065 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:11.255 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:11.591 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:00:12.315 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:00:13.750 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:00:15.714 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 108.181. Fitted coverage std. dev: 65.0594 0:00:15.715 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0555142 0:00:15.715 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 3 0:00:15.715 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 0:00:15.715 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 400 0:00:15.715 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 108.181 0:00:15.715 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 3 0:00:15.715 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:15.715 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:15.715 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:15.715 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:15.715 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:15.715 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:15.715 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:15.715 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.715 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.716 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:15.716 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:15.716 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:15.716 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:15.716 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.716 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.717 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.717 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.717 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:15.717 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:15.717 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:15.717 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:15.717 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 0:00:15.717 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:15.717 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta 0:00:15.717 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:15.717 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 15 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-lv6OTz/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 125 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-lv6OTz/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 0:00:00.000 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 0:00:00.002 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 86.1526 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: 2.60409 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.072 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:03.908 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:03.908 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.296 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:04.296 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.394 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.394 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.394 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.394 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.394 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:04.394 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:06.995 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. 0:00:07.492 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:07.882 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. 0:00:07.883 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:07.983 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:08.194 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:08.202 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). 0:00:08.202 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:08.283 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:08.284 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:08.285 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:08.370 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted 0:00:08.474 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:08.576 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:08.760 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:08.760 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:08.760 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:08.996 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:08.996 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:09.079 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:09.192 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:09.263 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 0:00:09.263 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 6 0:00:09.263 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 6. Coverage mad: 4.4478 0:00:09.263 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:09.277 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:09.377 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:09.508 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:09.702 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:09.833 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 0:00:09.834 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 2.02732e-07 0:00:09.834 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 1 0:00:09.834 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 1 0:00:09.834 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 238 0:00:09.834 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 13.7375 0:00:09.834 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 1 0:00:09.834 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:09.834 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:09.834 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:09.834 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:09.834 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:09.834 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:09.834 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:09.834 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:12.595 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. 0:00:13.086 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:13.398 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:13.399 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:13.487 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:13.694 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:13.696 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:13.696 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:13.779 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:13.780 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:13.780 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:13.867 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:13.868 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:13.868 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:13.868 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates 0:00:13.975 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:13.978 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:13.978 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:13.978 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:14.084 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:14.084 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:14.184 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:14.184 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:14.267 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:14.270 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:14.363 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times 0:00:14.364 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:14.364 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:14.364 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:14.365 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:14.365 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.467 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:00:14.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.487 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.564 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.589 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.589 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:14.589 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.590 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.663 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.665 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:14.665 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.665 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.665 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.666 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.666 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.666 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.666 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:14.666 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.667 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.667 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.667 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.672 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.672 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.672 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:14.672 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.672 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.673 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.673 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.673 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.673 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.673 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:14.673 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.674 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.674 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.674 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.674 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.674 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.681 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:14.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.682 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.682 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.682 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.683 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:14.683 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.683 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.683 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.683 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.687 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.688 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.688 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:14.688 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.688 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.688 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.689 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.689 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.689 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.689 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:14.689 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.689 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.690 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.690 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.690 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.690 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.690 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:14.690 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.695 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.695 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.787 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.787 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:14.887 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:14.887 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:14.887 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:14.888 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:14.888 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:14.888 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:14.888 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:14.888 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:17.683 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:18.285 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:18.603 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. 0:00:18.603 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:18.692 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:18.897 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:18.899 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). 0:00:18.906 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:18.988 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:18.989 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:18.989 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:19.167 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:19.168 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:19.168 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:19.168 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:19.190 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:19.190 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:19.190 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:19.190 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:19.190 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:19.190 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:19.292 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:19.292 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:19.371 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:19.371 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:19.491 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:19.491 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:19.574 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:19.574 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:19.574 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:19.687 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:19.688 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:19.688 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 0:00:19.688 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:00:19.688 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:19.688 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:19.867 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:00:19.868 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:00:19.868 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:00:19.869 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:19.870 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:19.870 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:19.871 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:19.871 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta 0:00:19.871 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:00:19.872 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:19.872 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:19.872 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 945 0:00:19.872 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:19.872 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:20.007 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:21.015 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:21.167 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:21.167 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges 0:00:21.169 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 0:00:21.260 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 0:00:21.262 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:21.279 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:21.280 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:21.280 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:21.366 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 0:00:21.385 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:21.474 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:21.493 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:00:21.493 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:21.493 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:21.493 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:21.583 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:21.584 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:21.584 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:21.584 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:21.584 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:21.584 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:21.766 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:21.883 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:21.884 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:00:21.884 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:00:21.975 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:21.976 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:21.976 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:21.976 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:00:21.976 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:00:21.977 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:21.977 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:21.977 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:21.977 64M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 0:00:21.978 64M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 0:00:21.978 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:21.978 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:21.978 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries 0:00:21.978 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 0:00:21.980 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:21.980 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:21.980 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:21.980 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:21.980 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:21.980 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:21.980 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:21.980 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:21.980 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:21.980 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:21.980 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:21.980 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:21.980 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:21.980 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:21.980 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:21.980 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:21.980 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:21.980 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:21.980 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:21.980 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:21.980 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:21.980 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:21.981 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths 0:00:21.981 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths 0:00:21.981 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:21.982 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 21 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Corrected reads are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/corrected/ * Assembled contigs are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/contigs.fasta * Assembled scaffolds are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/scaffolds.paths * Assembly graph is in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/spades.log Thank you for using SPAdes! /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/metaspades.py --test Command line: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/metaspades.py --test System information: SPAdes version: 3.13.1 Python version: 3.9.0 OS: Linux-5.10.0-8-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-lv6OTz/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/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/tmp Threads: 16 Memory limit (in Gb): 125 ======= SPAdes pipeline started. Log can be found here: /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/spades.log ===== Read error correction started. == Running read error correction tool: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-hammer /build/spades-lv6OTz/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-lv6OTz/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 125 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 Counting (kmer_data.cpp : 280) Estimating k-mer count 0:00:00.157 260M / 260M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:00.347 320M / 320M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:00.455 320M / 320M INFO K-mer Counting (kmer_data.cpp : 299) Total 4108 reads processed 0:00:01.564 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 0:00:01.565 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:02.859 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:04.047 1G / 1G INFO K-mer Counting (kmer_data.cpp : 331) Total 4108 reads processed 0:00:04.047 1G / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.047 1G / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.048 1G / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.048 1G / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.57642 Gb 0:00:04.048 1G / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:06.447 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:07.054 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:07.570 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed 0:00:08.101 1G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:08.471 1G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. 0:00:08.471 1G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:08.553 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:08.783 1G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:08.785 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). 0:00:08.844 64M / 10G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:00:08.857 64M / 10G INFO General (main.cpp : 148) Clustering Hamming graph. 0:00:09.151 64M / 10G INFO General (main.cpp : 155) Extracting clusters 0:00:09.267 64M / 10G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 0:00:09.268 64M / 10G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:00:09.268 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:09.672 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:10.067 64M / 10G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:00:10.067 64M / 10G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. 0:00:10.067 64M / 10G INFO General (main.cpp : 173) Subclustering Hamming graph 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 0:00:10.167 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 0:00:10.167 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)) 0:00:10.167 64M / 10G INFO General (main.cpp : 178) Finished clustering. 0:00:10.167 64M / 10G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. 0:00:10.372 64M / 10G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. 0:00:10.372 64M / 10G INFO General (main.cpp : 222) Solid k-mers finalized 0:00:10.372 64M / 10G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. 0:00:10.372 64M / 10G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:10.664 408M / 10G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. 0:00:10.854 408M / 10G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:00:10.948 408M / 10G INFO General (hammer_tools.cpp : 185) Written batch 0 0:00:11.062 64M / 10G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. 0:00:11.062 64M / 10G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. 0:00:11.063 64M / 10G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml 0:00:11.063 64M / 10G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/K21/configs/meta_mode.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 125 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-lv6OTz/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 0:00:00.183 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written 0:00:00.184 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads 0:00:00.304 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.305 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:00.430 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.432 4M / 140M INFO General (construction.cpp : 111) Max read length 100 0:00:00.432 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.432 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.432 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.453 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.453 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60409 Gb 0:00:00.453 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:03.487 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:04.168 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:04.168 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.683 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. 0:00:04.683 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.704 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.704 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.704 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.760 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.761 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:04.761 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:08.960 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. 0:00:09.991 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:10.303 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. 0:00:10.303 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:10.486 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.686 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:10.689 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). 0:00:10.689 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:10.780 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:10.781 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:10.781 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:10.781 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:10.964 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper 0:00:10.964 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:10.964 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:11.064 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:11.154 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:11.262 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:11.465 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:11.465 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:11.465 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:11.686 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). 0:00:11.686 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:11.864 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:11.962 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:11.962 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:11.962 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:11.963 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:12.056 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:12.056 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:12.162 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:12.162 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:12.266 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:12.267 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:12.365 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:12.366 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:12.366 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:12.366 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:12.366 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:12.366 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.384 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.384 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.470 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.471 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.660 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.660 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.660 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:12.660 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.680 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.680 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.772 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.773 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.876 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.876 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:12.876 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:12.876 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:12.876 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:12.961 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:12.961 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:13.060 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:13.061 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:13.160 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:13.160 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:13.258 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:13.259 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:13.281 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:13.282 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:13.374 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:13.375 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:13.470 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:13.471 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:13.566 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:13.567 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:13.660 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:13.661 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:13.756 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:13.756 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:13.856 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:13.857 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:13.953 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:13.953 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:13.976 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:13.977 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:14.079 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:14.079 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:14.262 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:14.262 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 0:00:14.363 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:14.364 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:14.464 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:14.465 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:14.465 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 0:00:14.465 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:14.465 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta 0:00:14.465 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:14.467 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 14 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-lv6OTz/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-lv6OTz/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-lv6OTz/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 125 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-lv6OTz/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 0:00:00.002 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: 2.60409 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:04.092 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:05.018 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:05.018 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.381 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. 0:00:05.381 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.509 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.509 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.509 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.510 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.510 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:05.510 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:08.655 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. 0:00:09.113 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.782 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. 0:00:09.782 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.885 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.080 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:10.081 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). 0:00:10.081 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:10.165 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:10.171 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:10.171 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:10.171 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:10.355 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper 0:00:10.355 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:10.355 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:10.474 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:10.567 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:10.671 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.847 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.848 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.848 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:11.175 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). 0:00:11.175 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:11.367 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:11.461 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:11.462 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:11.462 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:11.462 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:11.570 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:11.570 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:11.671 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:11.671 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:11.776 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:11.776 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:11.847 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:11.848 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:11.848 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:11.848 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:11.848 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:11.848 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.957 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.958 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.070 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.070 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.161 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.161 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.161 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.162 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.162 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.162 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.162 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.162 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:12.162 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.348 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.348 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.449 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.449 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.551 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.551 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:12.551 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:12.551 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:12.551 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:12.655 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:12.655 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:12.750 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:12.750 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:12.847 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:12.847 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:12.867 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:12.867 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.967 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.967 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:13.067 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:13.068 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:13.170 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:13.170 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:13.271 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:13.271 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:13.359 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:13.359 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:13.460 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:13.460 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:13.559 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:13.559 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:13.655 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:13.655 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:13.756 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:13.758 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:13.851 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:13.851 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:13.951 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:13.952 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:14.051 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:14.052 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 0:00:14.158 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:14.158 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:14.178 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:14.178 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:14.178 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 0:00:14.178 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:14.178 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta 0:00:14.179 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:14.179 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 14 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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 125 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-lv6OTz/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 0:00:00.000 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. 0:00:00.002 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: 2.60409 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.977 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:04.995 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:04.995 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.486 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:05.486 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.588 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.588 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.588 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.588 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.588 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:05.588 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:08.485 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. 0:00:09.004 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.400 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. 0:00:09.400 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.506 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:09.785 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:09.787 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). 0:00:09.787 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:09.789 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:09.790 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:09.790 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:09.880 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted 0:00:09.981 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:10.070 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.264 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.265 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.265 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.568 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:10.568 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:10.658 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:10.759 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:10.759 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:10.759 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.759 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:10.760 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:10.760 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:10.760 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:13.883 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. 0:00:14.518 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:15.080 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:15.080 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:15.214 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:15.476 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:15.485 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:15.485 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:15.557 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:15.558 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:15.558 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:15.681 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:15.681 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:15.681 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:15.682 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates 0:00:15.761 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:15.761 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:15.761 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:15.869 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:15.869 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:15.884 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:15.885 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:15.976 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:15.977 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage 0:00:16.080 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 0 times 0:00:16.081 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:16.176 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times 0:00:16.176 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification 0:00:16.176 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:16.176 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:16.176 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:16.177 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.276 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:00:16.276 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.363 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.364 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.468 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.469 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.469 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.469 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:16.469 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.560 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.576 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.682 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 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 StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:16.687 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:16.687 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:16.687 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:16.687 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:16.687 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:16.687 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:20.757 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:21.787 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:22.287 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. 0:00:22.287 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:22.388 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:22.571 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:22.573 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). 0:00:22.574 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:22.669 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:22.669 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:22.669 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:22.772 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:22.773 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:22.773 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:22.773 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:22.876 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting 0:00:22.877 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:22.877 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:22.877 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 0:00:22.877 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:22.878 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:23.088 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:24.159 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:24.326 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:24.327 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges 0:00:24.328 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 0:00:24.426 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 0:00:24.427 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:24.472 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:24.473 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:24.473 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:24.473 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 0:00:24.576 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:24.674 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:24.768 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation 0:00:24.768 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:24.768 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:24.768 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:24.773 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:24.781 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:24.781 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:24.781 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:24.781 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:24.781 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:25.059 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:25.255 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:25.255 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:00:25.255 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:00:25.280 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:25.354 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:25.354 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:25.354 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:00:25.355 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving 0:00:25.355 64M / 8G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings 0:00:25.355 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:25.356 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:25.356 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:25.357 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:25.357 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:25.357 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries 0:00:25.358 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 0:00:25.358 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:25.359 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:25.359 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:25.359 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:25.359 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:25.360 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:25.360 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:25.360 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:25.361 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:25.361 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:25.361 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:25.362 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:25.362 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:25.362 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:25.362 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:25.363 64M / 8G INFO General (repeat_resolving.cpp : 75) Restoring initial path extend settings 0:00:25.363 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:25.363 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:25.364 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:25.364 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:25.365 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths 0:00:25.365 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths 0:00:25.366 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Second Phase Setup 0:00:25.366 64M / 8G INFO General (second_phase_setup.cpp : 20) Preparing second phase 0:00:25.366 64M / 8G INFO General (second_phase_setup.cpp : 28) Moving preliminary contigs from /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/first_pe_contigs.fasta 0:00:25.366 64M / 8G INFO General (second_phase_setup.cpp : 40) Ready to run second phase 0:00:25.366 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:25.367 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:25.367 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:25.367 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:25.367 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:25.376 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:25.379 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:25.470 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:25.470 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:25.653 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:25.653 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:25.654 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:25.654 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:25.654 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:25.654 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:25.654 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:25.654 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:25.655 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:25.655 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:25.655 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:25.655 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:25.655 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:25.655 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:25.656 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:25.656 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:25.656 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:25.683 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:25.683 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:25.780 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:25.856 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:25.876 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:25.881 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:25.882 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:25.882 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:25.882 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:25.882 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:25.882 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:25.882 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:28.671 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:29.286 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:29.660 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. 0:00:29.661 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:29.782 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:29.990 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:29.992 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). 0:00:30.053 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:30.066 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:30.067 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:30.067 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:30.172 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:30.173 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:30.173 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:30.173 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:30.284 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:30.285 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:30.285 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:30.285 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:30.286 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:30.374 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:30.377 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:30.464 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:30.465 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:30.576 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:30.577 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:30.656 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:30.656 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:30.753 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:30.753 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:30.856 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:30.857 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:30.884 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:30.885 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:30.985 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:30.985 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:31.080 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:31.081 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:31.188 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:31.189 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:31.273 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:31.274 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:31.368 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:31.369 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:31.479 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:31.479 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:31.484 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:31.484 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:31.572 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:31.573 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:31.680 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:31.681 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:31.780 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:31.781 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:31.968 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:31.969 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 0:00:31.984 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:31.984 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:32.077 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:32.077 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:32.077 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 0:00:32.077 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:00:32.078 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:32.078 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:32.260 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:00:32.260 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:00:32.260 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:00:32.261 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:32.261 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:32.261 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:32.261 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:32.261 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta 0:00:32.262 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:00:32.262 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:32.262 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:32.262 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 0:00:32.262 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:32.262 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:32.474 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:33.505 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:33.631 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:33.631 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges 0:00:33.654 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 0:00:33.722 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 0:00:33.722 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:33.784 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:33.785 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:33.785 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:33.785 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 0:00:33.873 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:33.883 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:33.962 64M / 8G INFO General (pair_info_count.cpp : 330) Mapping contigs library #1 0:00:33.963 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:33.963 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 1 reads processed 0:00:33.963 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:00:33.963 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:33.964 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:33.964 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:34.053 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:34.062 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:34.063 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:34.063 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:34.065 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:34.065 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:34.176 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:34.388 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:34.388 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:00:34.388 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:00:34.482 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:34.484 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:34.484 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:34.484 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:00:34.484 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:00:34.484 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:34.484 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:34.484 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:34.484 64M / 8G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:00:34.484 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:34.484 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:34.484 64M / 8G INFO General (extenders_logic.cpp : 477) Using 1 single read library 0:00:34.484 64M / 8G INFO General (launcher.cpp : 359) Filling backbone edges for long reads scaffolding... 0:00:34.484 64M / 8G INFO General (launcher.cpp : 361) with long reads paths 0:00:34.484 64M / 8G INFO General (launcher.cpp : 370) Removing fake unique with paired-end libs 0:00:34.484 64M / 8G INFO General (launcher.cpp : 381) 0 unique edges 0:00:34.484 64M / 8G INFO General (extenders_logic.cpp : 389) Using 0 long reads scaffolding libraries 0:00:34.484 64M / 8G INFO General (extenders_logic.cpp : 399) Using additional coordinated coverage extender 0:00:34.484 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 0:00:34.485 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:34.485 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:34.485 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:34.485 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:34.485 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:34.485 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:34.485 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:34.485 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:34.485 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:34.485 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:34.485 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:34.485 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:34.485 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:34.485 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:34.485 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:34.485 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:34.485 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:34.485 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:34.485 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:34.485 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:34.485 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:34.485 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:34.486 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths 0:00:34.486 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths 0:00:34.487 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:34.487 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 34 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Corrected reads are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/corrected/ * Assembled contigs are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/contigs.fasta * Assembled scaffolds are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/scaffolds.paths * Assembly graph is in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/spades.log Thank you for using SPAdes! /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/rnaspades.py --test Command line: /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/rnaspades.py --test System information: SPAdes version: 3.13.1 Python version: 3.9.0 OS: Linux-5.10.0-8-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-lv6OTz/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/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/tmp Threads: 16 Memory limit (in Gb): 125 ======= SPAdes pipeline started. Log can be found here: /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/spades.log /build/spades-lv6OTz/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100 /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/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-lv6OTz/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 125 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-lv6OTz/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 0:00:00.103 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written 0:00:00.105 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads 0:00:00.238 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.238 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:00.408 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.409 4M / 140M INFO General (construction.cpp : 111) Max read length 100 0:00:00.409 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1611 0:00:00.410 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.410 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.410 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.410 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60409 Gb 0:00:00.410 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.511 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:04.065 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:04.065 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.416 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 974 kmers in total. 0:00:04.416 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.508 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.508 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.508 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.508 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.508 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:04.508 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:07.203 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 974 kmers. 0:00:07.722 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:08.024 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 975 kmers in total. 0:00:08.024 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:08.106 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:08.308 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:08.310 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.2133 bits per kmer). 0:00:08.310 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:08.403 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:08.403 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:08.403 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:08.403 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:08.587 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 7 34-mers were removed by early tip clipper 0:00:08.587 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:08.587 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:08.691 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:08.703 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:08.803 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:08.987 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:08.987 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:08.988 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:09.210 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.3614 bits per kmer). 0:00:09.210 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:09.404 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:09.501 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:09.501 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 72 0:00:09.501 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage 0:00:09.502 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 225.865 0:00:09.502 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 22.5865 0:00:09.502 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 22.5865 0:00:09.502 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:09.502 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:09.502 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:09.503 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:09.503 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:09.603 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:09.603 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:00:09.603 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT 0:00:09.796 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times 0:00:09.796 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:00:09.895 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:00:09.895 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:09.987 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:09.987 64M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections 0:00:09.988 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 0:00:09.988 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 0:00:09.988 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:09.988 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:09.989 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:09.989 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:09.989 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:09.989 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.089 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.089 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:10.179 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:10.179 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.209 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.209 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:10.307 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:10.307 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:10.308 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:10.308 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.399 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.399 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:10.491 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:10.491 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.583 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.589 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:10.683 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:10.683 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:10.684 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:10.684 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.778 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.779 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:10.811 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:10.811 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.903 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.903 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.005 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.006 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.006 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:11.006 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.105 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.105 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.191 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.191 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.295 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.295 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.403 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.403 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.404 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:11.404 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.487 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.487 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.587 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.587 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.598 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.598 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.707 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.707 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.707 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:11.707 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.797 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.798 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.909 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.909 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.983 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.983 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.087 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:12.087 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.088 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:12.095 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.186 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.187 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:12.279 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:12.279 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.308 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.308 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.393 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:12.407 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.407 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:12.407 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.491 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.491 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:12.599 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:12.599 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.679 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.786 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:12.787 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.795 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:12.796 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.887 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.887 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:12.983 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:12.983 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:13.083 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:13.083 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:13.184 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:13.185 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:13.185 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:13.185 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:13.278 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:13.279 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:13.303 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:13.303 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:13.476 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:13.476 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:13.504 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:13.504 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:13.504 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:13.504 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:13.603 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:13.603 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:13.711 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:13.711 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:13.884 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:13.891 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:13.976 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:13.976 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:13.976 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:13.976 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:13.977 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:13.977 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:13.977 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:13.977 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:13.977 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:14.000 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:14.001 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:14.101 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:14.101 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:14.187 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:14.187 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:14.279 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:14.279 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:14.395 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:14.396 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:14.495 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:14.495 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:14.603 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:14.604 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:14.607 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:14.607 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:14.783 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:14.783 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:14.807 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:14.807 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:14.903 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:14.903 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.000 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.000 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:15.087 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:15.087 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.195 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.196 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:15.295 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:15.295 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:15.387 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:15.387 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:15.387 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:15.491 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:15.491 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:15.492 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.865 0:00:15.492 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:15.492 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta 0:00:15.493 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:15.493 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 15 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-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/spades_test/K49/configs/rna_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 125 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-lv6OTz/spades-3.13.1+dfsg/spades_test/dataset.info) with K=49 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 0:00:00.000 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 0:00:00.002 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: 2.60409 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:04.062 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:05.221 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:05.221 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.656 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. 0:00:05.656 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.687 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.687 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.687 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.688 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.688 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:05.688 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:10.063 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 958 kmers. 0:00:10.800 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:11.170 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 959 kmers in total. 0:00:11.170 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:11.254 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:11.468 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:11.469 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (81.4849 bits per kmer). 0:00:11.469 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:11.569 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:11.571 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:11.571 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:11.654 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 5 sequences extracted 0:00:11.747 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:11.854 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:11.975 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:11.976 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:11.976 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:12.262 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.5031 bits per kmer). 0:00:12.262 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:12.345 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:12.461 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:12.461 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 53 0:00:12.461 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage 0:00:12.461 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 162.219 0:00:12.461 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 16.2219 0:00:12.461 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 16.2219 0:00:12.461 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:12.461 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:12.461 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:12.461 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:12.461 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:12.461 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:12.462 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:12.462 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:16.346 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 10 sequences. 0:00:16.915 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:17.268 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. 0:00:17.269 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:17.359 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:17.575 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:17.648 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.5031 bits per kmer). 0:00:17.648 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:17.664 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:17.665 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:17.665 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:17.751 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:17.751 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:17.751 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:17.751 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:17.863 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:17.864 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:17.864 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:17.864 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:17.943 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:17.943 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:00:17.943 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT 0:00:18.143 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times 0:00:18.146 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:00:18.158 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:00:18.158 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:18.343 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1 times 0:00:18.344 64M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections 0:00:18.344 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 0:00:18.344 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 0:00:18.344 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:18.345 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:18.345 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:18.345 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:18.345 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:18.345 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:18.443 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:00:18.443 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:18.463 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:18.464 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:18.553 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:18.559 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:18.560 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:18.560 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:18.560 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:18.560 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:18.561 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:18.561 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:18.646 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:18.647 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:18.647 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:18.647 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:18.751 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:18.752 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:18.850 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:18.850 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:18.866 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:18.867 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:18.951 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:18.952 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:18.952 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:18.952 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:19.055 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:19.056 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:19.163 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:19.164 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:19.263 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:19.263 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:19.356 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:19.356 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:19.356 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:19.356 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:19.463 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:19.464 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:19.546 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:19.546 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:19.666 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:19.667 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:19.751 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:19.751 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:19.751 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:19.751 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:19.843 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:19.843 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:19.959 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:19.960 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:20.051 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:20.051 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:20.067 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:20.068 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:20.068 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:20.068 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:20.244 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:20.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:20.259 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:20.260 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:20.366 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:20.366 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:20.459 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:20.460 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:20.460 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:20.460 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:20.546 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:20.547 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:20.644 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:20.645 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:20.670 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:20.670 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:20.747 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:20.747 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:20.747 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:20.747 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:20.850 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:20.851 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:20.947 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:20.947 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:21.047 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:21.048 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:21.155 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:21.156 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:21.156 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:21.156 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:21.256 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:21.256 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:21.267 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:21.267 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:21.356 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:21.357 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:21.461 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:21.461 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:21.461 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:21.461 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:21.567 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:21.568 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:21.647 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:21.648 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:21.743 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:21.744 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:21.847 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:21.848 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:21.848 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:21.848 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:21.866 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:21.866 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:21.962 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:21.962 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:22.146 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:22.146 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:22.154 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:22.154 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:22.154 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:22.154 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:22.155 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:22.155 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:22.155 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:22.155 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60286 Gb 0:00:22.155 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:25.672 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:26.511 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:26.864 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. 0:00:26.864 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:26.977 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:27.171 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:27.173 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (82.103 bits per kmer). 0:00:27.174 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:27.251 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:27.252 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:27.252 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:27.347 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:27.347 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:27.347 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:27.347 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:27.467 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:27.468 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:27.468 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:27.468 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:27.468 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:27.468 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:27.468 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:27.549 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:27.549 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:27.575 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:27.575 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:27.765 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:27.765 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:27.775 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:27.840 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:27.867 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:27.870 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:27.967 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:27.968 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:28.050 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:28.050 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:28.147 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:28.147 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:28.255 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:28.255 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:28.348 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:28.349 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:28.455 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:28.456 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:28.551 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:28.552 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:28.567 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:28.568 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:28.663 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:28.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:28.760 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:28.760 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:28.851 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:28.854 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:28.854 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:28.951 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:28.952 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:28.952 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 163.37 0:00:28.952 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:00:28.952 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:28.953 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:29.069 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:00:29.069 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:00:29.069 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:00:29.069 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:29.069 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa 0:00:29.069 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta 0:00:29.069 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg 0:00:29.070 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/final_contigs.fasta 0:00:29.070 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:00:29.070 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:29.070 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:29.070 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 951 0:00:29.070 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:29.070 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:29.311 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:30.214 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:30.366 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:30.366 336M / 8G INFO General (pair_info_count.cpp : 211) 1751 paired reads (85.2483% of all) aligned to long edges 0:00:30.368 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 0:00:30.368 64M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:30.368 64M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:30.368 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 0:00:30.375 76M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:30.451 76M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:30.467 64M / 8G INFO General (pair_info_count.cpp : 395) Mapping single reads of library #0 0:00:30.467 64M / 8G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:00:30.467 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:30.559 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 4108 reads processed 0:00:30.560 64M / 8G INFO General (pair_info_count.cpp : 397) Total paths obtained from single reads: 0 0:00:30.560 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:00:30.560 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:30.560 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:30.560 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:30.662 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:30.662 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:30.662 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:30.663 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:30.663 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:30.663 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:30.855 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:31.050 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:31.051 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:00:31.051 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:31.051 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:31.068 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:31.068 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:31.068 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:31.068 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries 0:00:31.068 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 0:00:31.069 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:31.069 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:31.069 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:31.069 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:31.069 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:31.069 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:31.069 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:31.069 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:31.069 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:31.069 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:31.069 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:31.069 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:31.069 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:31.069 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:31.069 64M / 8G INFO General (launcher.cpp : 466) Finalizing paths - hard 0:00:31.069 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:00:31.069 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:00:31.069 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 0:00:31.069 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 0:00:31.069 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 0:00:31.069 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 0:00:31.069 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 0:00:31.069 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 0:00:31.069 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 0:00:31.069 64M / 8G INFO General (launcher.cpp : 466) Finalizing paths - soft 0:00:31.069 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 56 0:00:31.069 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 56 0:00:31.069 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 56 0:00:31.069 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:00:31.069 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:00:31.069 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 0:00:31.069 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 71 0:00:31.069 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 71 0:00:31.069 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 71 0:00:31.069 64M / 8G INFO General (launcher.cpp : 474) Finalizing main paths 0:00:31.070 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 81 0:00:31.070 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 81 0:00:31.070 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 81 0:00:31.070 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 111 0:00:31.070 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 111 0:00:31.070 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 111 0:00:31.070 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:00:31.070 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:00:31.070 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 0:00:31.070 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:31.070 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:31.070 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa 0:00:31.070 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta 0:00:31.070 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg 0:00:31.070 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test//K49/transcripts.paths 0:00:31.071 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:31.072 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 31 seconds ===== Assembling finished. Used k-mer sizes: 33, 49 * Assembled transcripts are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/transcripts.paths * Hard filtered transcripts are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/soft_filtered_transcripts.fasta * Assembly graph is in /build/spades-lv6OTz/spades-3.13.1+dfsg/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-lv6OTz/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-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/truspades.py --test # Cleunup symlinks rm -rf /build/spades-lv6OTz/spades-3.13.1+dfsg/../share/ unlink /build/spades-lv6OTz/spades-3.13.1+dfsg/install_spades/bin/spades-bwa make[1]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3 --sourcedirectory=assembler/src --buildsystem=cmake dh_testroot -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_prep -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_auto_install make[1]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' echo "Nothing to install" Nothing to install find /build/spades-lv6OTz/spades-3.13.1+dfsg -name *.pyc -delete make[1]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg' debian/rules override_dh_installdocs make[1]: Entering directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/spades-lv6OTz/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-lv6OTz/spades-3.13.1+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' mkdir -p /build/spades-lv6OTz/spades-3.13.1+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/spades-lv6OTz/spades-3.13.1+dfsg/debian/man_src/*.adoc cp /build/spades-lv6OTz/spades-3.13.1+dfsg/debian/man_src/*.? /build/spades-lv6OTz/spades-3.13.1+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/spades-lv6OTz/spades-3.13.1+dfsg' dh_python3 -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installinit -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installsystemduser -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_perl -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_link -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_link: warning: skipping link from usr/bin/spades to self dh_strip_nondeterminism -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_compress -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_fixperms -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_missing -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_dwz -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_strip -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_makeshlibs -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_shlibdeps -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installdeb -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_gencontrol -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_md5sums -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_builddeb -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dpkg-deb: building package 'spades-dbgsym' in '../spades-dbgsym_3.13.1+dfsg-2+b2_amd64.deb'. dpkg-deb: building package 'spades' in '../spades_3.13.1+dfsg-2+b2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../spades_3.13.1+dfsg-2+b2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/spades-lv6OTz /tmp/spades-3.13.1+dfsg-2+b2k533iexg I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.FGYy2dUtLp... I: success in 5856.8962 seconds md5: spades-dbgsym_3.13.1+dfsg-2+b2_amd64.deb: OK md5: Value of 'md5' differs for spades_3.13.1+dfsg-2+b2_amd64.deb sha1: spades-dbgsym_3.13.1+dfsg-2+b2_amd64.deb: OK sha1: Value of 'sha1' differs for spades_3.13.1+dfsg-2+b2_amd64.deb sha256: spades-dbgsym_3.13.1+dfsg-2+b2_amd64.deb: OK sha256: Value of 'sha256' differs for spades_3.13.1+dfsg-2+b2_amd64.deb Checksums: FAIL diffoscope run passed