Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/spades/spades_3.15.4+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/spades-3.15.4+dfsg-1rim78oqn/spades_3.15.4+dfsg-1_amd64.buildinfo Get source package info: spades=3.15.4+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/spades/3.15.4+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=asciidoctor=2.0.16-2 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bwa=0.7.17-7 bzip2=1.0.8-5 ca-certificates=20211016 cmake=3.23.0-1 cmake-data=3.23.0-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-19 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-python=5.20220403 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-3 findutils=4.9.0-2 g++=4:11.2.0-2 g++-11=11.2.0-19 gcc=4:11.2.0-2 gcc-11=11.2.0-19 gcc-11-base=11.2.0-19 gcc-12-base=12-20220319-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 icu-devtools=67.1-7 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libarchive13=3.6.0-1 libasan6=11.2.0-19 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbam-dev=0.1.19+dfsg-5 libbamtools-dev=2.5.1+dfsg-10+b1 libbamtools2.5.1=2.5.1+dfsg-10+b1 libbinutils=2.38-3 libblkid1=2.37.3-1+b1 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbwa-dev=0.7.17-7 libbz2-1.0=1.0.8-5 libbz2-dev=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libclang-cpp13=1:13.0.1-3+b2 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcurl3-gnutls=7.82.0-2 libcurl4=7.82.0-2 libcurl4-gnutls-dev=7.82.0-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdeflate-dev=1.10-2 libdeflate0=1.10-2 libdpkg-perl=1.21.7 libedit2=3.1-20210910-1 libelf1=0.186-1 libexpat1=2.4.8-1 libffi-dev=3.4.2-4 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-19 libgcc-s1=12-20220319-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgssapi-krb5-2=1.19.2-2+b1 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-2 libhts3=1.13+ds-2 libhtscodecs2=1.2.1-1 libicu-dev=67.1-7 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12-20220319-1 libjsoncpp25=1.9.5-4 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 libldap-2.5-0=2.5.11+dfsg-1 libllvm13=1:13.0.1-3+b2 liblsan0=12-20220319-1 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2.1 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-3 libmagic1=1:5.41-3 libmd0=1.0.4-1 libmount1=2.37.3-1+b1 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses-dev=6.3-2 libncurses6=6.3-2 libncursesw6=6.3-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnlopt-cxx-dev=2.7.1-3 libnlopt-cxx0=2.7.1-3 libnlopt-dev=2.7.1-3 libnlopt0=2.7.1-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-4 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpfm4=4.11.1+git32-gd0b85fb-1 libpipeline1=1.5.5-1 libprocps8=2:3.3.17-7+b1 libpsl5=0.21.0-1.2 libpython3-stdlib=3.10.4-1 libpython3.10-minimal=3.10.4-3 libpython3.10-stdlib=3.10.4-3 libpython3.9-minimal=3.9.12-1 libpython3.9-stdlib=3.9.12-1 libquadmath0=12-20220319-1 libreadline8=8.1.2-1 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libruby3.0=3.0.3-1 libsasl2-2=2.1.28+dfsg-2+b1 libsasl2-modules-db=2.1.28+dfsg-2+b1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.38.2-1 libssh2-1=1.10.0-3 libssl1.1=1.1.1n-1 libssw-dev=1.1-13 libssw0=1.1-13 libstdc++-11-dev=11.2.0-19 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtinfo-dev=6.3-2 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-3 libtsan0=11.2.0-19 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libuv1=1.44.1-2 libxml2=2.9.13+dfsg-1 libxml2-dev=2.9.13+dfsg-1 libyaml-0-2=0.2.2-1 libz3-4=4.8.12-1+b1 libz3-dev=4.8.12-1+b1 libzstd1=1.4.10+dfsg-1 linux-libc-dev=5.16.18-1 llvm=1:13.0-54 llvm-13=1:13.0.1-3+b2 llvm-13-dev=1:13.0.1-3+b2 llvm-13-linker-tools=1:13.0.1-3+b2 llvm-13-runtime=1:13.0.1-3+b2 llvm-13-tools=1:13.0.1-3+b2 llvm-dev=1:13.0-54 llvm-runtime=1:13.0-54 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 lynx=2.9.0dev.10-1 lynx-common=2.9.0dev.10-1 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.1.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 openssl=1.1.1n-1 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 po-debconf=1.0.21+nmu1 procps=2:3.3.17-7+b1 python3=3.10.4-1 python3-all=3.10.4-1 python3-distutils=3.9.12-1 python3-joblib=0.17.0-4 python3-lib2to3=3.9.12-1 python3-minimal=3.10.4-1 python3-pkg-resources=59.6.0-1.2 python3-pygments=2.11.2+dfsg-2 python3-yaml=5.4.1-1+b1 python3.10=3.10.4-3 python3.10-minimal=3.10.4-3 python3.9=3.9.12-1 python3.9-minimal=3.9.12-1 rake=13.0.6-3 readline-common=8.1.2-1 rpcsvc-proto=1.4.2-4 ruby=1:3.0+1 ruby-asciidoctor=2.0.16-2 ruby-net-telnet=0.1.1-2 ruby-rubygems=3.3.5-2 ruby-xmlrpc=0.3.2-1 ruby3.0=3.0.3-1 rubygems-integration=1.18 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tzdata=2022a-1 util-linux=2.37.3-1+b1 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --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/20220415T025620Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220415T025620Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220411T155650Z/ 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=3.15.4+dfsg-1 && mkdir -p /build/spades-lUTA64 && dpkg-source --no-check -x /*.dsc /build/spades-lUTA64/spades-3.15.4+dfsg && chown -R builduser:builduser /build/spades-lUTA64" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/spades-lUTA64/spades-3.15.4+dfsg && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649705433" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/spades-lUTA64 /tmp/spades-3.15.4+dfsg-1rim78oqn bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220411T155650Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.Za_uUK5iUv 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.Za_uUK5iUv Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220411T155650Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220411T155650Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1076 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 ... 4701 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220415T025620Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220415T025620Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220411T155650Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Za_uUK5iUv Get:1 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220411T155650Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main Sources [12.0 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main amd64 Packages [11.4 MB] Fetched 23.5 MB in 20s (1170 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.Za_uUK5iUv I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d spades=3.15.4+dfsg-1 && mkdir -p /build/spades-lUTA64 && dpkg-source --no-check -x /*.dsc /build/spades-lUTA64/spades-3.15.4+dfsg && chown -R builduser:builduser /build/spades-lUTA64"' exec /tmp/mmdebstrap.Za_uUK5iUv 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 9932 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main spades 3.15.4+dfsg-1 (dsc) [2350 B] Get:2 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main spades 3.15.4+dfsg-1 (tar) [9901 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220415T025620Z bookworm/main spades 3.15.4+dfsg-1 (diff) [29.1 kB] Fetched 9932 kB in 8s (1270 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'spades_3.15.4+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting spades in /build/spades-lUTA64/spades-3.15.4+dfsg dpkg-source: info: unpacking spades_3.15.4+dfsg.orig.tar.xz dpkg-source: info: unpacking spades_3.15.4+dfsg-1.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 0114_use_debian_provided_libs.patch dpkg-source: info: applying 0118_adjust_spades_home_again.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying python3.patch dpkg-source: info: applying yaml_load.patch dpkg-source: info: applying debuginfo.patch dpkg-source: info: applying debian_bwa_zlib.patch dpkg-source: info: applying workdir_for_test.patch dpkg-source: info: applying disable_local_convertutf.patch dpkg-source: info: applying fix-sigill-on-non-popcnt-cpus.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/spades-lUTA64/spades-3.15.4+dfsg && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649705433" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.Za_uUK5iUv dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.15.4+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --sourcedirectory=assembler/src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg' dh_auto_clean find . -name "*.pyc" -delete rm -rf /build/spades-lUTA64/spades-3.15.4+dfsg/debian/man_src/*.html /build/spades-lUTA64/spades-3.15.4+dfsg/debian/man_src/*.? rm -rf /build/spades-lUTA64/spades-3.15.4+dfsg/debian/man make[1]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg' dh_autoreconf_clean -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg' dh_clean -X.orig make[1]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg' debian/rules binary-arch dh binary-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-lUTA64/spades-3.15.4+dfsg' dh_auto_configure -- -DBoost_NO_BOOST_CMAKE=TRUE cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBoost_NO_BOOST_CMAKE=TRUE ../assembler/src CMake Warning (dev) in CMakeLists.txt: No project() command is present. The top-level CMakeLists.txt file must contain a literal, direct call to the project() command. Add a line of code such as project(ProjectName) near the top of the file, but after cmake_minimum_required(). CMake is pretending there is a "project(Project)" command on the first line. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so - found -- Found Boost: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include (found version "1.63.0") Making Release Configuration... Building SPAdes from N/A, sha: N/A -- Override standard malloc (MI_OVERRIDE=ON) -- Enable abort() calls on memory allocation failure (MI_XMALLOC=ON) -- Enable printing of error and warning messages by default (MI_SHOW_ERRORS=ON) -- Use the C++ compiler to compile (MI_USE_CXX=ON) -- -- Library base name: mimalloc-none -- Build type : none -- Compiler : /usr/bin/c++ -- Install directory: /usr/lib/mimalloc-1.6 -- Build targets : object -- -- Looking for open -- Looking for open - found -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for cxxabi.h -- Looking for cxxabi.h - not found -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for mach/mach.h -- Looking for mach/mach.h - not found -- Looking for link.h -- Looking for link.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for sys/mman.h -- Looking for sys/mman.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for malloc/malloc.h -- Looking for malloc/malloc.h - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Looking for futimens -- Looking for futimens - found -- Looking for futimes -- Looking for futimes - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for mallinfo -- Looking for mallinfo - found -- Looking for mallctl -- Looking for mallctl - not found -- Looking for malloc_zone_statistics -- Looking for malloc_zone_statistics - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Looking for pthread_getspecific in pthread -- Looking for pthread_getspecific in pthread - found -- Looking for pthread_rwlock_init in pthread -- Looking for pthread_rwlock_init in pthread - found -- Looking for pthread_mutex_lock in pthread -- Looking for pthread_mutex_lock in pthread - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.13") -- Looking for include file endian.h -- Looking for include file endian.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file strings.h -- Looking for include file strings.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file sys/param.h -- Looking for include file sys/param.h - found -- Looking for include file sys/sysctl.h -- Looking for include file sys/sysctl.h - not found -- Looking for include file emmintrin.h -- Looking for include file emmintrin.h - found -- Looking for include file pmmintrin.h -- Looking for include file pmmintrin.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for chmod -- Looking for chmod - found -- Looking for fseeko -- Looking for fseeko - found -- Looking for fstat -- Looking for fstat - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for getpid -- Looking for getpid - found -- Looking for mkstemp -- Looking for mkstemp - found -- Looking for popen -- Looking for popen - found -- Looking for putenv -- Looking for putenv - found -- Looking for stat -- Looking for stat - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for sysctl -- Looking for sysctl - not found -- Looking for times -- Looking for times - found -- Looking for erfc -- Looking for erfc - not found CMake Deprecation Warning at /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Found PythonInterp: /usr/bin/python3.10 (found version "3.10.4") CMake Deprecation Warning at projects/mts/CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg' dh_auto_build -- all debruijn_test include_test cd obj-x86_64-linux-gnu && make -j10 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -B/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/getopt_pp /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake --color= make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/cppformat /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gfa1 /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gfa1 /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/edlib /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake --color= 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-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o -MF CMakeFiles/gfa1.dir/gfa.c.o.d -o CMakeFiles/gfa1.dir/gfa.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gfa1/gfa.c make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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ext/cppformat/CMakeFiles/format.dir/format.cc.o make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/cppformat -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wall -Wextra -pedantic -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/cppformat/format.cc make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build [ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -MF CMakeFiles/llvm-support.dir/APFloat.cpp.o.d -o CMakeFiles/llvm-support.dir/APFloat.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/APFloat.cpp [ 1%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. 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/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/easel.c cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -std=c++14 -MD -MT ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/src/gtest-all.cc /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c:610:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 610 | printf("%02llx ", j); | ~~~~~^ ~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %02lx /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c:641:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 641 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 642 | qf->metadata->nblocks, | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c:641:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 641 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 642 | qf->metadata->nblocks, 643 | qf->metadata->ndistinct_elts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c:641:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 641 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu ...... 644 | qf->metadata->nelts); | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include/gqf/gqf.h: In function 'qf_deserialize': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c:1606:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1606 | fread(qf->metadata, sizeof(qfmetadata), 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf/gqf.c:1615:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1615 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 2%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o -MF CMakeFiles/easel.dir/esl_alphabet.c.o.d -o CMakeFiles/easel.dir/esl_alphabet.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_alphabet.c [ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -MF CMakeFiles/ConsensusCore.dir/Coverage.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Coverage.cpp [ 2%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_avx.c [ 2%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_buffer.c [ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -MF CMakeFiles/ConsensusCore.dir/Mutation.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Mutation.cpp [ 2%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -MF CMakeFiles/easel.dir/esl_cluster.c.o.d -o CMakeFiles/easel.dir/esl_cluster.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_cluster.c [ 2%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_composition.c [ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_dirichlet.c [ 3%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp [ 3%] Linking C static library libgqf.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/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 [ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_distance.c [ 3%] Linking C static library libgfa1.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 /usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o /usr/bin/ranlib libgqf.a /usr/bin/ranlib libgfa1.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 3%] Built target gqf 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-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/coverage_model /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 3%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include 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'/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 3%] Linking CXX static library libgetopt_pp.a [ 3%] Built target gfa1 make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake --color= cd 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[ 4%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -MF CMakeFiles/binary_io.dir/graph_pack.cpp.o.d -o CMakeFiles/binary_io.dir/graph_pack.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/static.c:28: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/region.c: In function 'void _mi_mem_collect(mi_os_tld_t*)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/region.c:466:15: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'mem_region_t' {aka 'struct mem_region_s'} with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] 466 | memset(®ions[i], 0, sizeof(mem_region_t)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/region.c:89:16: note: 'mem_region_t' {aka 'struct mem_region_s'} declared here 89 | typedef struct mem_region_s { | ^~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/static.c:31: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/heap.c: In function 'mi_heap_t* mi_heap_new()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/heap.c:196:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] 196 | memcpy(heap, &_mi_heap_empty, sizeof(mi_heap_t)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include/mimalloc-internal.h:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/static.c:17: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc.c:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/static.c:32: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c: At global scope: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:71:42: note: in expansion of macro 'MI_FORWARD1' 71 | void* malloc(size_t size) MI_FORWARD1(mi_malloc, size); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:72:42: note: in expansion of macro 'MI_FORWARD2' 72 | void* calloc(size_t size, size_t n) MI_FORWARD2(mi_calloc, size, n); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:73:42: note: in expansion of macro 'MI_FORWARD2' 73 | void* realloc(void* p, size_t newsize) MI_FORWARD2(mi_realloc, p, newsize); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:95:55: note: in expansion of macro 'MI_FORWARD1' 95 | void* operator new(std::size_t n) noexcept(false) MI_FORWARD1(mi_new,n); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:96:55: note: in expansion of macro 'MI_FORWARD1' 96 | void* operator new[](std::size_t n) noexcept(false) MI_FORWARD1(mi_new,n); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:167:42: note: in expansion of macro 'MI_FORWARD2' 167 | void* reallocf(void* p, size_t newsize) MI_FORWARD2(mi_reallocf,p,newsize); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:168:42: note: in expansion of macro 'MI_FORWARD1' 168 | size_t malloc_size(const void* p) MI_FORWARD1(mi_usable_size,p); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:170:42: note: in expansion of macro 'MI_FORWARD1' 170 | size_t malloc_usable_size(void *p) MI_FORWARD1(mi_usable_size,p); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:194:53: note: in expansion of macro 'MI_FORWARD1' 194 | void* __libc_malloc(size_t size) MI_FORWARD1(mi_malloc,size); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:195:53: note: in expansion of macro 'MI_FORWARD2' 195 | void* __libc_calloc(size_t count, size_t size) MI_FORWARD2(mi_calloc,count,size); | ^~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:196:53: note: in expansion of macro 'MI_FORWARD2' 196 | void* __libc_realloc(void* p, size_t size) MI_FORWARD2(mi_realloc,p,size); | ^~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/static.c:38: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/init.c: In function 'bool _mi_heap_init()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/init.c:192:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] 192 | memcpy(heap, &_mi_heap_empty, sizeof(*heap)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include/mimalloc-internal.h:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/src/static.c:17: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ [ 4%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/BamReader.cpp [ 5%] Linking CXX static library libedlib.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 /usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o /usr/bin/ranlib libedlib.a [ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_dmatrix.c make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 5%] Built target edlib make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 5%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/version.cpp [ 6%] Linking CXX static library libversion.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 /usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o /usr/bin/ranlib libversion.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 6%] Built target version make -f common/sequence/CMakeFiles/sequence.dir/build.make 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common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -MF CMakeFiles/sequence.dir/sequence_tools.cpp.o.d -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/sequence_tools.cpp [ 8%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o -MF CMakeFiles/BamTools.dir/BamWriter.cpp.o.d -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/BamWriter.cpp [ 8%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/cppformat -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wall -Wextra -pedantic -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/cppformat/CMakeFiles/format.dir/posix.cc.o -MF CMakeFiles/format.dir/posix.cc.o.d -o CMakeFiles/format.dir/posix.cc.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/cppformat/posix.cc [ 8%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp [ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_dsqdata.c [ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_exponential.c [ 9%] Linking CXX static library libformat.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 /usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o [ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_fileparser.c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:14: note: did you mean to dereference the pointer? 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^ /usr/bin/ranlib libformat.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o -MF CMakeFiles/BamTools.dir/SamProgram.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/SamProgram.cpp [ 11%] Built target format 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-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 11%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/distance_estimation.cpp [ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_gamma.c [ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_gencode.c [ 11%] Linking CXX static library libsequence.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 /usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o /usr/bin/ranlib libsequence.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 11%] Built target sequence make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 11%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_reader.cpp [ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp [ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_getopts.c [ 11%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/APInt.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, io::binary::FullPackIO::Type&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] 363 | bool loaded = base::BinRead(is, gp); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:207:19: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::EdgesPositionHandler]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:210:45: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] 101 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:213:34: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::KmerMapper]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:216:35: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:219:41: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:253:22: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:256:45: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 130 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:259:34: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:262:35: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:265:41: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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_ ? | ^~~~~~~ [ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_gev.c [ 11%] Built target mimalloc-obj make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/mapping_printer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 11%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/PairwiseAlignment.cpp [ 11%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -MF CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o.d -o CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp [ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/SamReadGroup.cpp [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_gumbel.c [ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_heap.c [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_histogram.c In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(omnigraph::ConstructionHelper::VertexId, omnigraph::ConstructionHelper::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; omnigraph::ConstructionHelper::VertexId = omnigraph::impl::VertexId; omnigraph::ConstructionHelper::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(omnigraph::ConstructionHelper::EdgeId, omnigraph::ConstructionHelper::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; omnigraph::ConstructionHelper::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -MF CMakeFiles/ConsensusCore.dir/Sequence.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp [ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_hmm.c [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -MF CMakeFiles/ConsensusCore.dir/Utils.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Utils.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp [ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_hyperexp.c [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o -MF CMakeFiles/ConsensusCore.dir/Version.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Version.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Version.cpp [ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/SamSequenceDictionary.cpp [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_keyhash.c [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_mem.c [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_minimizer.c [ 16%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_writer.cpp [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_mixgev.c [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_mpi.c [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msa.c [ 17%] Linking CXX static library libcoverage_model.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 /usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp /usr/bin/ranlib libcoverage_model.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 17%] Built target coverage_model make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 17%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o -MF CMakeFiles/utils.dir/memory_limit.cpp.o.d -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/memory_limit.cpp [ 17%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -MF CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -MF CMakeFiles/easel.dir/esl_msacluster.c.o.d -o CMakeFiles/easel.dir/esl_msacluster.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msacluster.c [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile.c [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile2.c [ 17%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -MF CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp [ 17%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Atomic.cpp [ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/CrashRecoveryContext.cpp [ 18%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/fastg_writer.cpp [ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile_a2m.c [ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Debug.cpp [ 18%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -MF CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile_afa.c [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c [ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Errno.cpp [ 19%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp [ 20%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp [ 20%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c [ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Error.cpp [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp [ 22%] Linking CXX static library libgraphio.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o [ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile_selex.c /usr/bin/ranlib libgraphio.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 22%] Built target graphio [ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -MF CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c [ 22%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -MF CMakeFiles/easel.dir/esl_msashuffle.c.o.d -o CMakeFiles/easel.dir/esl_msashuffle.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msashuffle.c [ 23%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_msaweight.c [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_normal.c [ 23%] Linking CXX static library libmapping_printer.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -P CMakeFiles/mapping_printer.dir/cmake_clean_target.cmake [ 23%] Linking CXX static library ../../../lib/libgtest.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake /usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_paml.c /usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" /usr/bin/ranlib libmapping_printer.a [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_random.c /usr/bin/ranlib ../../../lib/libgtest.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 23%] Built target mapping_printer [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_randomseq.c make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 25%] Built target gtest [ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_ratematrix.c [ 25%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp [ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/FoldingSet.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_recorder.c [ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp [ 27%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/filesystem/temporary.cpp [ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_regexp.c [ 27%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/filesystem/glob.cpp [ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_rootfinder.c [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_scorematrix.c [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_sq.c [ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o cd 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/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Hashing.cpp [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_sqio.c make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 29%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -std=c++14 -MD -MT ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc [ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Host.cpp [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c [ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/JSON.cpp [ 29%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c [ 30%] Linking CXX static library ../../../lib/libgtest_main.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp [ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/LEB128.cpp /usr/bin/ranlib ../../../lib/libgtest_main.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 31%] Built target gtest_main make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/teamcity_gtest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 31%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/logger/logger_impl.cpp [ 31%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_sse.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_ssi.c [ 32%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp [ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Locale.cpp [ 32%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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-Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp [ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/MD5.cpp [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_stats.c [ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp [ 32%] Linking CXX static library libteamcity_gtest.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_stopwatch.c /usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o /usr/bin/ranlib libteamcity_gtest.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 32%] Built target teamcity_gtest [ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_stretchexp.c [ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_threads.c [ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/MemAlloc.cpp [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_tree.c [ 36%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_vectorops.c [ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp [ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -MF CMakeFiles/easel.dir/esl_vmx.c.o.d -o CMakeFiles/easel.dir/esl_vmx.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_vmx.c [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_weibull.c [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_workqueue.c [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel/esl_wuss.c [ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Path.cpp [ 37%] Linking C static library libeasel.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 /usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o CMakeFiles/easel.dir/esl_distance.c.o CMakeFiles/easel.dir/esl_dmatrix.c.o CMakeFiles/easel.dir/esl_dsqdata.c.o CMakeFiles/easel.dir/esl_exponential.c.o CMakeFiles/easel.dir/esl_fileparser.c.o CMakeFiles/easel.dir/esl_gamma.c.o CMakeFiles/easel.dir/esl_gencode.c.o CMakeFiles/easel.dir/esl_getopts.c.o CMakeFiles/easel.dir/esl_gev.c.o CMakeFiles/easel.dir/esl_gumbel.c.o CMakeFiles/easel.dir/esl_heap.c.o CMakeFiles/easel.dir/esl_histogram.c.o CMakeFiles/easel.dir/esl_hmm.c.o CMakeFiles/easel.dir/esl_hyperexp.c.o CMakeFiles/easel.dir/esl_keyhash.c.o CMakeFiles/easel.dir/esl_mem.c.o CMakeFiles/easel.dir/esl_minimizer.c.o CMakeFiles/easel.dir/esl_mixgev.c.o CMakeFiles/easel.dir/esl_mpi.c.o CMakeFiles/easel.dir/esl_msa.c.o CMakeFiles/easel.dir/esl_msacluster.c.o CMakeFiles/easel.dir/esl_msafile.c.o CMakeFiles/easel.dir/esl_msafile2.c.o CMakeFiles/easel.dir/esl_msafile_a2m.c.o CMakeFiles/easel.dir/esl_msafile_afa.c.o CMakeFiles/easel.dir/esl_msafile_clustal.c.o CMakeFiles/easel.dir/esl_msafile_phylip.c.o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o CMakeFiles/easel.dir/esl_msafile_selex.c.o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o CMakeFiles/easel.dir/esl_msashuffle.c.o CMakeFiles/easel.dir/esl_msaweight.c.o CMakeFiles/easel.dir/esl_normal.c.o CMakeFiles/easel.dir/esl_paml.c.o CMakeFiles/easel.dir/esl_random.c.o CMakeFiles/easel.dir/esl_randomseq.c.o CMakeFiles/easel.dir/esl_ratematrix.c.o CMakeFiles/easel.dir/esl_recorder.c.o CMakeFiles/easel.dir/esl_regexp.c.o CMakeFiles/easel.dir/esl_rootfinder.c.o CMakeFiles/easel.dir/esl_scorematrix.c.o CMakeFiles/easel.dir/esl_sq.c.o CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_vmx.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o /usr/bin/ranlib libeasel.a [ 37%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp [ 37%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' 578 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 37%] Built target easel [ 37%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ [ 37%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c [ 37%] Linking CXX static library libutils.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: /build/spades-lUTA64/spades-3.15.4+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); | ^~~~~~~~~~~ cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a [ 38%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: /build/spades-lUTA64/spades-3.15.4+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); | ^~~~~~~~~~~ [ 38%] Built target utils make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c [ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.cpp [ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o [ 40%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -MF CMakeFiles/hmmer.dir/src/build.c.o.d -o CMakeFiles/hmmer.dir/src/build.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/build.c cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Program.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /build/spades-lUTA64/spades-3.15.4+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); | ^~~~~~~~~~~ [ 40%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: At top level: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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); | ^~~~~~~~~~~~~~~ [ 40%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: /build/spades-lUTA64/spades-3.15.4+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); | ^~~~~~~~~~~ [ 40%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c [ 40%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -MF CMakeFiles/hmmer.dir/src/cachedb.c.o.d -o CMakeFiles/hmmer.dir/src/cachedb.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/cachedb.c [ 40%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -MF CMakeFiles/hmmer.dir/src/emit.c.o.d -o CMakeFiles/hmmer.dir/src/emit.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/emit.c [ 41%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: /build/spades-lUTA64/spades-3.15.4+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); | ^~~~~~~~~~~ [ 41%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp [ 41%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o -MF CMakeFiles/hmmer.dir/src/errors.c.o.d -o CMakeFiles/hmmer.dir/src/errors.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/errors.c [ 41%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o -MF CMakeFiles/hmmer.dir/src/evalues.c.o.d -o CMakeFiles/hmmer.dir/src/evalues.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/evalues.c [ 41%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/genomic_info.cpp [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Regex.cpp [ 43%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o -MF CMakeFiles/hmmer.dir/src/eweight.c.o.d -o CMakeFiles/hmmer.dir/src/eweight.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/eweight.c [ 43%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o -MF CMakeFiles/hmmer.dir/src/generic_decoding.c.o.d -o CMakeFiles/hmmer.dir/src/generic_decoding.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_decoding.c In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.cpp:100: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.inc:94:10: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] 94 | mi = ::mallinfo(); | ^~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.inc:35, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.cpp:100: /usr/include/malloc.h:118:24: note: declared here 118 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; | ^~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.cpp:100: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] 94 | mi = ::mallinfo(); | ~~~~~~~~~~^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.inc:35, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Process.cpp:100: /usr/include/malloc.h:118:24: note: declared here 118 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; | ^~~~~~~~ [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o [ 43%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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-DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_fwdback.c [ 43%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_fwdback_banded.c [ 43%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_null2.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_null2.c.o -MF CMakeFiles/hmmer.dir/src/generic_null2.c.o.d -o CMakeFiles/hmmer.dir/src/generic_null2.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_null2.c [ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.c.o -MF CMakeFiles/hmmer.dir/src/generic_msv.c.o.d -o CMakeFiles/hmmer.dir/src/generic_msv.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_msv.c [ 44%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp [ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o -MF CMakeFiles/hmmer.dir/src/generic_optacc.c.o.d -o CMakeFiles/hmmer.dir/src/generic_optacc.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_optacc.c [ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_stotrace.c [ 44%] Linking CXX static library libpaired_info.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 /usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/SmallVector.cpp [ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -MF CMakeFiles/hmmer.dir/src/generic_viterbi.c.o.d -o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_viterbi.c [ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_vtrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/generic_vtrace.c [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/SourceMgr.cpp /usr/bin/ranlib libpaired_info.a [ 45%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o -MF CMakeFiles/hmmer.dir/src/h2_io.c.o.d -o CMakeFiles/hmmer.dir/src/h2_io.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/h2_io.c make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 45%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o -MF CMakeFiles/hmmer.dir/src/heatmap.c.o.d -o CMakeFiles/hmmer.dir/src/heatmap.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/heatmap.c [ 45%] Built target paired_info [ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/StringExtras.cpp [ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -MF CMakeFiles/hmmer.dir/src/hmmlogo.c.o.d -o CMakeFiles/hmmer.dir/src/hmmlogo.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/hmmlogo.c [ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/StringMap.cpp [ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/hmmdwrkr.c [ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdmstr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c [ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -MF CMakeFiles/hmmer.dir/src/hmmdutils.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdutils.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/hmmdutils.c [ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -MF CMakeFiles/hmmer.dir/src/hmmer.c.o.d -o CMakeFiles/hmmer.dir/src/hmmer.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/hmmer.c [ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/logsum.c [ 47%] Linking CXX static library libbinary_io.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 /usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o [ 47%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp /usr/bin/ranlib libbinary_io.a [ 47%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp [ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -MF CMakeFiles/hmmer.dir/src/modelconfig.c.o.d -o CMakeFiles/hmmer.dir/src/modelconfig.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/modelconfig.c make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 47%] Built target binary_io [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -MF CMakeFiles/hmmer.dir/src/modelstats.c.o.d -o CMakeFiles/hmmer.dir/src/modelstats.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/modelstats.c cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/StringSaver.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp [ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -MF CMakeFiles/hmmer.dir/src/mpisupport.c.o.d -o CMakeFiles/hmmer.dir/src/mpisupport.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/mpisupport.c [ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/seqmodel.c [ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -MF CMakeFiles/hmmer.dir/src/tracealign.c.o.d -o CMakeFiles/hmmer.dir/src/tracealign.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/tracealign.c [ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_alidisplay.c [ 50%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Threading.cpp [ 50%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp [ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -MF CMakeFiles/hmmer.dir/src/p7_bg.c.o.d -o CMakeFiles/hmmer.dir/src/p7_bg.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_bg.c [ 50%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -MF CMakeFiles/hmmer.dir/src/p7_builder.c.o.d -o CMakeFiles/hmmer.dir/src/p7_builder.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_builder.c [ 51%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/Unicode.cpp [ 52%] Linking CXX static library libBamTools.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/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 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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 [ 52%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/WithColor.cpp [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_domaindef.c [ 53%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o [ 53%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/YAMLParser.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 53%] Built target BamTools [ 53%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp [ 53%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/raw_ostream.cpp [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o -MF CMakeFiles/hmmer.dir/src/p7_gbands.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gbands.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_gbands.c [ 53%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/regcomp.c [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxb.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_gmxb.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src 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ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/regerror.c [ 54%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o [ 55%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong 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-ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/regexec.c [ 55%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm/regstrlcpy.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include 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-c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_hmmcache.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem 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/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_null3.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -MF CMakeFiles/hmmer.dir/src/p7_pipeline.c.o.d -o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_pipeline.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o -MF CMakeFiles/hmmer.dir/src/p7_prior.c.o.d -o CMakeFiles/hmmer.dir/src/p7_prior.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_prior.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o -MF CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_profile.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_spensemble.c make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 56%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/kstring.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -MF CMakeFiles/hmmer.dir/src/p7_tophits.c.o.d -o CMakeFiles/hmmer.dir/src/p7_tophits.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_tophits.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -MF CMakeFiles/hmmer.dir/src/p7_trace.c.o.d -o CMakeFiles/hmmer.dir/src/p7_trace.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_trace.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -MF CMakeFiles/hmmer.dir/src/p7_scoredata.c.o.d -o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/p7_scoredata.c [ 58%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_aux.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -MF CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o.d -o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/hmmpgmd2msa.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -MF CMakeFiles/hmmer.dir/src/fm_alphabet.c.o.d -o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/fm_alphabet.c [ 58%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam.c [ 59%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_import.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -MF CMakeFiles/hmmer.dir/src/fm_general.c.o.d -o CMakeFiles/hmmer.dir/src/fm_general.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/fm_general.c [ 60%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam.c.o -MF CMakeFiles/samtools.dir/sam.c.o.d -o CMakeFiles/samtools.dir/sam.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/sam.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/fm_sse.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/fm_ssv.c [ 60%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_core': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:178:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 60%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_pileup.c [ 60%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_lpileup.c [ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_md.c [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/decoding.c [ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c: In function '_razf_write': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_close': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_end_flush': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c: In function 'save_zindex': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/fwdback.c [ 61%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/faidx.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/io.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/io.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/ssvfilter.c [ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bedidx.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/msvfilter.c [ 62%] Linking CXX static library libConsensusCore.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 /usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_md.c: In function 'bam_prob_realn_core': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_md.c:214:35: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 214 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_md.c:198:19: note: at offset -2 into destination object of size [0, 9223372036854775807] allocated by 'bam_aux_get' 198 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | ^~~~~~~~~~~~~~~~~~~~ [ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_sort.c /usr/bin/ranlib libConsensusCore.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 62%] Built target ConsensusCore make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake --color= [ 63%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/sam_header.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/null2.c make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 63%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp [ 63%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_reheader.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c [ 63%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/kprobaln.c [ 63%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/mismatch_correction.cpp [ 63%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/pair_info_count.cpp [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c [ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/second_phase_setup.cpp [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_omx.c [ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/distance_estimation.cpp [ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/repeat_resolving.cpp [ 66%] Linking CXX static library libllvm-support.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 /usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" [ 66%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools/bam_cat.c /usr/bin/ranlib libllvm-support.a [ 66%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c [ 66%] Linking CXX static library libsamtools.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/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-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 66%] Built target llvm-support [ 66%] Built target samtools make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend [ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/contig_output_stage.cpp make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/id_distributor.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:27:9: warning: unused variable 'code' [-Wunused-variable] 27 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); | ^~~~ [ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::{anonymous}::CollectLibInformation(const debruijn_graph::GraphPack&, size_t&, size_t, size_t)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/pair_info_count.cpp:235:42: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 235 | if (data.median_insert_size < gp.k() + 2) | ~~~~~~~^~~ [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/chromosome_removal.cpp [ 68%] Linking C static library libhmmer.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o /usr/bin/ranlib libhmmer.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target hmmer make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 68%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/reads/parser.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, long unsigned int>]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:103:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(debruijn_graph::SplitPathConstructor::EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::SplitPathConstructor::EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:230:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:102:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:93:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/distance_estimation.cpp:165:31: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:28:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 28 | size_t min_dist, | ~~~~~~~^~~~~~~~ [ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] 457 | bool u1 = UpdateLeft(gap, split_orig, split_res); | ^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:458:14: warning: unused variable 'u2' [-Wunused-variable] 458 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(debruijn_graph::gap_closing::HybridGapCloser::gap_info_it, debruijn_graph::gap_closing::HybridGapCloser::gap_info_it) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] 630 | size_t cur_len = end_it - start_it; | ^~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ [ 68%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/reads/paired_readers.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp:394:46: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/extract_domains.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_matcher.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 69%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/reads/binary_converter.cpp [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_matcher.cpp: In function 'void nrps::match_contigs_internal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const string&, const string&, const string&, nrps::ContigAlnInfo&, io::OFastaReadStream&, size_t)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_matcher.cpp:55:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 55 | if (seqpos2.second - seqpos2.first < model_length / 10) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/histogram.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:20, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: while referencing 'tmp' 580 | value_type tmp(std::forward(args)...); | ^~~ [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/load_graph.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 216 | for (;index != res.first; ++index) { | ~~~~~~^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, debruijn_graph::DomainGraphConstructor::PairComparator> >&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 243 | if (coords.second + 5000 > path.Length()) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ [ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp [ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/domain_graph.cpp [ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/reads/binary_streams.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: while referencing 'tmp' 580 | value_type tmp(std::forward(args)...); | ^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: while referencing 'tmp' 580 | value_type tmp(std::forward(args)...); | ^~~ [ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/reads/io_helper.cpp make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/hmm /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/hmm /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 72%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/hmm/hmmfile.cpp [ 72%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp [ 72%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/hmm/hmmmatcher.cpp [ 72%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 161 | pli->Z = pli->domZ = cfg.Z; | ~~~~^ [ 72%] Linking CXX static library libhmmercpp.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o /usr/bin/ranlib libhmmercpp.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 72%] Built target hmmercpp [ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp [ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp [ 73%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/sam/read.cpp [ 74%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/sam/sam_reader.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': /usr/include/c++/11/bits/stl_vector.h:942:43: required from 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type) [with _Tp = debruijn_graph::EdgeInfo; _Alloc = std::allocator >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:163:21: required from 'void utils::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:43:21: required from 'void utils::PerfectHashMapBuilder::BuildIndex(utils::PerfectHashMap&, const KMerStorage&, size_t) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:144:39: required from 'void utils::BuildIndex(utils::PerfectHashMap&, const KMerStorage&, size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:249:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const Graph&) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:27:39: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const Graph&) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:31:64: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:20:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 20 | IdHolder edge_id_; | ^~~~~~~~ [ 74%] Linking CXX static library libinput.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 74%] Built target input In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/sequence.hpp:132:28: warning: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::from_' may be used uninitialized in this function [-Wmaybe-uninitialized] 132 | : size_(size), from_(from), rtl_(rtl), data_(seq.data_) {} | ^~~~~~~~~~~ In file included from /usr/include/c++/11/bits/nested_exception.h:40, from /usr/include/c++/11/exception:154, from /usr/include/c++/11/ios:39, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/11/bits/move.h:204:11: note: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::from_' was declared here 204 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/sequence.hpp:132:15: warning: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::size_' may be used uninitialized in this function [-Wmaybe-uninitialized] 132 | : size_(size), from_(from), rtl_(rtl), data_(seq.data_) {} | ^~~~~~~~~~~ In file included from /usr/include/c++/11/bits/nested_exception.h:40, from /usr/include/c++/11/exception:154, from /usr/include/c++/11/ios:39, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/11/bits/move.h:204:11: note: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::size_' was declared here 204 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/sequence.hpp:132:41: warning: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::rtl_' may be used uninitialized in this function [-Wmaybe-uninitialized] 132 | : size_(size), from_(from), rtl_(rtl), data_(seq.data_) {} | ^~~~~~~~~ In file included from /usr/include/c++/11/bits/nested_exception.h:40, from /usr/include/c++/11/exception:154, from /usr/include/c++/11/ios:39, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/11/bits/move.h:204:11: note: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::rtl_' was declared here 204 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/sequence.hpp:182:14: warning: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::rtl_' may be used uninitialized in this function [-Wmaybe-uninitialized] 182 | rtl_ = rhs.rtl_; | ~~~~~^~~~~~~~~~ In file included from /usr/include/c++/11/bits/nested_exception.h:40, from /usr/include/c++/11/exception:154, from /usr/include/c++/11/ios:39, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/11/bits/move.h:204:11: note: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::rtl_' was declared here 204 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/sequence.hpp:180:15: warning: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::from_' may be used uninitialized in this function [-Wmaybe-uninitialized] 180 | from_ = rhs.from_; | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/c++/11/bits/nested_exception.h:40, from /usr/include/c++/11/exception:154, from /usr/include/c++/11/ios:39, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/11/bits/move.h:204:11: note: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::from_' was declared here 204 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/sequence.hpp:181:15: warning: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::size_' may be used uninitialized in this function [-Wmaybe-uninitialized] 181 | size_ = rhs.size_; | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/c++/11/bits/nested_exception.h:40, from /usr/include/c++/11/exception:154, from /usr/include/c++/11/ios:39, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/11/bits/move.h:204:11: note: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::size_' was declared here 204 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ [ 74%] Linking CXX static library libassembly_graph.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 /usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 74%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o [ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.cpp [ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o [ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -MF CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d -o CMakeFiles/modules.dir/alignment/gap_info.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/gap_info.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -MF CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -MF CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp [ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp [ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:277:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 277 | if (bad_mapping_pos == -1) | ~~~~~~~~~~~~~~~~^~~~~ [ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.cpp:34:58: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, omnigraph::de::PairedIndexHandler::EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedIndexHandler::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp [ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp [ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp [ 77%] Linking CXX static library libspades-stages.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 /usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target spades-stages [ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp [ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp [ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp [ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp [ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp [ 81%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp: In static member function 'static int path_extend::ExtenderTriplet::GetPriority(io::LibraryType)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:34:13: note: in expansion of macro 'SET_PRIORITY' 34 | SET_PRIORITY(LibraryType::SangerReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' 35 | SET_PRIORITY(LibraryType::PacBioReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' 35 | SET_PRIORITY(LibraryType::PacBioReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' 36 | SET_PRIORITY(LibraryType::NanoporeReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' 36 | SET_PRIORITY(LibraryType::NanoporeReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' 37 | SET_PRIORITY(LibraryType::TrustedContigs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' 37 | SET_PRIORITY(LibraryType::TrustedContigs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' 38 | SET_PRIORITY(LibraryType::SingleReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' 38 | SET_PRIORITY(LibraryType::SingleReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' 39 | SET_PRIORITY(LibraryType::PairedEnd); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' 39 | SET_PRIORITY(LibraryType::PairedEnd); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' 40 | SET_PRIORITY(LibraryType::HQMatePairs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' 40 | SET_PRIORITY(LibraryType::HQMatePairs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' 41 | SET_PRIORITY(LibraryType::MatePairs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' 41 | SET_PRIORITY(LibraryType::MatePairs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' 42 | SET_PRIORITY(LibraryType::TSLReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' 42 | SET_PRIORITY(LibraryType::TSLReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' 43 | SET_PRIORITY(LibraryType::PathExtendContigs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' 43 | SET_PRIORITY(LibraryType::PathExtendContigs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' 44 | SET_PRIORITY(LibraryType::UntrustedContigs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' 44 | SET_PRIORITY(LibraryType::UntrustedContigs); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' 45 | SET_PRIORITY(LibraryType::FLRNAReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' 45 | SET_PRIORITY(LibraryType::FLRNAReads); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:46:13: note: in expansion of macro 'SET_PRIORITY' 46 | SET_PRIORITY(LibraryType::AssemblyGraph); | ^~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 111 | if (iter->second < min_read_count_) { | ^~~~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 81%] Linking CXX static library libmodules.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 /usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o /usr/bin/ranlib libmodules.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target modules [ 81%] Linking CXX static library libpath_extend.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 /usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/graph_pack.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/library.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/library_data.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/config_struct.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/stage.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/genomic_quality.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/graph_pack.cpp:11: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(debruijn_graph::KmerMapper::EdgeId, debruijn_graph::KmerMapper::EdgeId, debruijn_graph::KmerMapper::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::KmerMapper::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 82%] Linking CXX static library libpipeline.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeline.dir/link.txt --verbose=1 /usr/bin/ar qc libpipeline.a CMakeFiles/pipeline.dir/config_struct.cpp.o CMakeFiles/pipeline.dir/graph_pack.cpp.o CMakeFiles/pipeline.dir/library.cpp.o CMakeFiles/pipeline.dir/library_data.cpp.o CMakeFiles/pipeline.dir/stage.cpp.o /usr/bin/ranlib libpipeline.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 82%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/construction.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -MF CMakeFiles/stages.dir/read_conversion.cpp.o.d -o CMakeFiles/stages.dir/read_conversion.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/read_conversion.cpp [ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -MF CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/genomic_info_filler.cpp [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/subcluster.cpp [ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/ss_edge_split.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/kmer_helpers.cpp [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/config_struct.cpp [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const string&, const string&, float&, float&, int)': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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(); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': /build/spades-lUTA64/spades-3.15.4+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; | ~~~~~~~~~~^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/hkmer.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/kmer_data.hpp:16, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/HSeq.hpp: In instantiation of 'static size_t hammer::HSeq::GetDataSize(size_t) [with long unsigned int N = 16; size_t = long unsigned int]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:175:52: required from 'void kmers::KMerDiskStorage::merge() [with S = hammer::HSeq<16>; traits = kmers::kmer_index_traits >]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:446:25: required from 'auto kmers::KMerIndexBuilder::BuildIndex(Index&, kmers::KMerCounter&, bool) [with Index = kmers::KMerIndex > >; typename Index::KMerSeq = hammer::HSeq<16>]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:172:102: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/HSeq.hpp:93:36: warning: unused parameter 'size' [-Wunused-parameter] 93 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -MF CMakeFiles/spades-ionhammer.dir/main.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/main.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/construction.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/construction.cpp:357:110: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/reference.cpp [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, omnigraph::EdgeProcessingAlgorithm::ProceedConditionT) [with Priority = adt::identity; Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgeProcessingAlgorithm::ProceedConditionT = func::TypedPredicate]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:328:94: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:345:28: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:474:24: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, omnigraph::EdgeProcessingAlgorithm::ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgeProcessingAlgorithm::ProceedConditionT = func::TypedPredicate]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:83:52: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/ionhammer/main.cpp:90:3: warning: control reaches end of non-void function [-Wreturn-type] 90 | } | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:17: /build/spades-lUTA64/spades-3.15.4+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 = omnigraph::impl::VertexId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:100:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+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 = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+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::allocator >&)>]' /usr/include/c++/11/ext/new_allocator.h:162:4: 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::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper]' /usr/include/c++/11/bits/alloc_traits.h:516:17: 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::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper; std::allocator_traits >::allocator_type = std::allocator >]' /usr/include/c++/11/bits/shared_ptr_base.h:519:39: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/11/bits/shared_ptr_base.h:1342:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' /usr/include/c++/11/bits/shared_ptr.h:409:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper]' /usr/include/c++/11/bits/shared_ptr.h:862:14: 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::allocator >&)>&}]' /usr/include/c++/11/bits/shared_ptr.h:878:39: 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::allocator >&)>&}]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:492:65: required from 'omnigraph::AlgoPtr debruijn::simplification::ComplexTipClipperInstance(Graph&, debruijn_graph::config::debruijn_config::simplification::complex_tip_clipper, const debruijn::simplification::SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:248:42: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:43:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 43 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:17: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(omnigraph::simplification::relative_coverage::Component::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::Component::VertexId = omnigraph::impl::VertexId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(omnigraph::simplification::relative_coverage::Component::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::Component::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::HandlerF, size_t, std::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' /usr/include/c++/11/ext/new_allocator.h:162:4: required from 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /usr/include/c++/11/bits/alloc_traits.h:516:17: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/11/bits/shared_ptr_base.h:1342:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' /usr/include/c++/11/bits/shared_ptr.h:409:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /usr/include/c++/11/bits/shared_ptr.h:862:14: required from 'std::shared_ptr<_Tp> std::allocate_shared(const _Alloc&, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}]' /usr/include/c++/11/bits/shared_ptr.h:878:39: required from 'std::shared_ptr<_Tp> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const debruijn::simplification::SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:237:57: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:17: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector::BulgeInfo>&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::ParallelBulgeRemover::SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:17: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(omnigraph::complex_br::ComplexBulgeRemover::VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(omnigraph::complex_br::ComplexBulgeRemover::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:777:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 777 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(omnigraph::complex_br::ComponentProjector::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComponentProjector::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:824:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(omnigraph::complex_br::ComplexBulgeRemover::VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(omnigraph::complex_br::ComplexBulgeRemover::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:793:16: warning: unused variable 'end_height' [-Wunused-variable] 793 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(omnigraph::complex_br::SkeletonTree::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::SkeletonTree::VertexId = omnigraph::impl::VertexId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:32: warning: unused parameter 'v' [-Wunused-parameter] 309 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, omnigraph::complex_br::SkeletonTree::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; omnigraph::complex_br::SkeletonTree::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:320:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:322:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 322 | for (EdgeId e : old_edges) { | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(omnigraph::complex_br::ComponentColoring::EdgeId, omnigraph::complex_br::ComponentColoring::EdgeId, omnigraph::complex_br::ComponentColoring::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComponentColoring::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:18: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:71: warning: unused parameter 'edge2' [-Wunused-parameter] 476 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/spades-lUTA64/spades-3.15.4+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 = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:241:18: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ [ 86%] Linking CXX executable ../../bin/spades-ionhammer cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-ionhammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o" "CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o" "CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o" "CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o" "CMakeFiles/spades-ionhammer.dir/main.cpp.o" "CMakeFiles/spades-ionhammer.dir/reference.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o" "CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o" "CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o" "CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-ionhammer ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a /usr/lib/x86_64-linux-gnu/libz.so ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a -lssw ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target spades-ionhammer In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 86%] Linking CXX static library libstages.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -E cmake_link_script CMakeFiles/stages.dir/link.txt --verbose=1 /usr/bin/ar qc libstages.a CMakeFiles/stages.dir/read_conversion.cpp.o CMakeFiles/stages.dir/construction.cpp.o CMakeFiles/stages.dir/simplification.cpp.o CMakeFiles/stages.dir/ss_edge_split.cpp.o CMakeFiles/stages.dir/genomic_info_filler.cpp.o /usr/bin/ranlib libstages.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 86%] Building CXX object common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -MF CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o.d -o CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/concurrent_dsu.cpp [ 86%] Linking CXX static library libcommon_modules.a cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common && /usr/bin/cmake -E cmake_link_script CMakeFiles/common_modules.dir/link.txt --verbose=1 /usr/bin/ar qc libcommon_modules.a CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o /usr/bin/ranlib libcommon_modules.a make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target common_modules make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake --color= make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake --color= make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/scaffold_correction /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake --color= make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake --color= make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_converter /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake --color= cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gbuilder /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gbuilder /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gmapper /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build [ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/main.cpp make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build [ 86%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o [ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o [ 87%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount/read_filter.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/positional_read.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gbuilder -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -MF CMakeFiles/spades-gbuilder.dir/main.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gbuilder/main.cpp make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o [ 87%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_converter -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -MF CMakeFiles/spades-gmapper.dir/main.cpp.o.d -o CMakeFiles/spades-gmapper.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper/main.cpp [ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/pipeline.cpp make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/scaffold_correction/main.cpp make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp [ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/kmercount/main.cpp [ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(spades::StageManager&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/pipeline.cpp:135:19: warning: unused variable 'mode' [-Wunused-variable] 135 | pipeline_type mode = cfg::get().mode; | ^~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper/main.cpp:29: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] 457 | bool u1 = UpdateLeft(gap, split_orig, split_res); | ^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:458:14: warning: unused variable 'u2' [-Wunused-variable] 458 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper/main.cpp:29: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(debruijn_graph::gap_closing::HybridGapCloser::gap_info_it, debruijn_graph::gap_closing::HybridGapCloser::gap_info_it) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] 630 | size_t cur_len = end_it - start_it; | ^~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ [ 89%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/contig_processor.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper/main.cpp:16: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ^~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gbuilder/main.cpp:24: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gbuilder/main.cpp:24: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 89%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/main.cpp [ 89%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/hammer_tools.cpp [ 89%] Linking CXX executable ../../bin/spades-kmer-estimating cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so [ 89%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 89%] Built target spades-convert-bin-to-fasta [ 89%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/hamcluster.cpp make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 89%] Built target spades-kmer-estimating make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 89%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -MF CMakeFiles/unitig-coverage.dir/main.cpp.o.d -o CMakeFiles/unitig-coverage.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/main.cpp [ 89%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/dataset_processor.cpp [ 89%] Linking CXX executable ../../bin/spades-truseq-scfcorrection cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:543:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/hamcluster.cpp:54:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const string&, const KMerData&, dsu::ConcurrentDSU&)::]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/hamcluster.cpp:147:21: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:42: warning: unused parameter 'num_elems' [-Wunused-parameter] 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~~~~^~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ [ 90%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spades/series_analysis.cpp make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 90%] Built target spades-truseq-scfcorrection make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/spaligner.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o -MF CMakeFiles/spaligner.dir/align_longreads.cpp.o.d -o CMakeFiles/spaligner.dir/align_longreads.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/align_longreads.cpp [ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/easel -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/mts/contig_abundance.cpp [ 94%] Linking CXX executable ../../bin/spades-read-filter cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 357 | for (uint32_t j=0; j::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 94%] Built target spades-read-filter make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -MF CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o.d -o CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp [ 94%] Linking CXX executable ../../bin/spades-kmercount cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target spades-kmercount make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/config_struct.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/corrector/main.cpp [ 95%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/globals.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/hammer_tools.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:11: In member function 'void NibbleString::set(size_t, uint8_t) [with unsigned int N = 21; unsigned int bits = 6; Storage = long unsigned int]', inlined from 'NibbleString::NibbleString(const uint8_t*) [with unsigned int N = 21; unsigned int bits = 6; Storage = long unsigned int]' at /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_stat.hpp:62:16, inlined from 'KMerStat::KMerStat(uint32_t, float, const unsigned char*)' at /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_stat.hpp:121:96, inlined from 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)' at /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:433:81: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_stat.hpp:69:40: warning: 'kms.KMerStat::qual.NibbleString<21, 6, long unsigned int>::storage_.std::array::_M_elems[0]' may be used uninitialized [-Wmaybe-uninitialized] 69 | storage_[idx] = (storage_[idx] & ~(MaxValue << offset)) | ((value & MaxValue) << offset); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:433:22: note: 'kms' declared here 433 | KMerStat kms(0 /* cnt */, 1.0 /* total quality */, NULL /*quality */); | ^~~ [ 95%] Linking CXX executable ../../bin/spades-gmapper cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -MF CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp [ 95%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/kmer_data.cpp make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target spades-gmapper make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -MF CMakeFiles/cds-mapping-stats.dir/stats.cpp.o.d -o CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(debruijn_graph::KmerMapper::EdgeId, debruijn_graph::KmerMapper::EdgeId, debruijn_graph::KmerMapper::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::KmerMapper::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:21: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 96%] Linking CXX executable ../../bin/spades-corrector-core cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target spades-corrector-core [ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const debruijn::simplification::SimplifInfoContainer&, bool, const std::function&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] 103 | const bool using_edge_qual = edge_qual.IsAttached(); | ^~~~~~~~~~~~~~~ [ 96%] Linking CXX executable ../../bin/spades-core cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm [ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/main.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(omnigraph::simplification::relative_coverage::Component::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::Component::VertexId = omnigraph::impl::VertexId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(omnigraph::simplification::relative_coverage::Component::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::Component::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::HandlerF, size_t, std::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' /usr/include/c++/11/ext/new_allocator.h:162:4: required from 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /usr/include/c++/11/bits/alloc_traits.h:516:17: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/11/bits/shared_ptr_base.h:1342:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' /usr/include/c++/11/bits/shared_ptr.h:409:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /usr/include/c++/11/bits/shared_ptr.h:862:14: required from 'std::shared_ptr<_Tp> std::allocate_shared(const _Alloc&, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}]' /usr/include/c++/11/bits/shared_ptr.h:878:39: required from 'std::shared_ptr<_Tp> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const debruijn::simplification::SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:157:65: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:12: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector::BulgeInfo>&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::ParallelBulgeRemover::SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] [ 96%] Linking CXX executable ../../bin/spades-gbuilder cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target spades-core make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/depend make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/build make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -MF CMakeFiles/mag-improve.dir/main.cpp.o.d -o CMakeFiles/mag-improve.dir/main.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/main.cpp make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target spades-gbuilder [ 96%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const VertexSet&, const EdgeSet&, const EdgeSet&) const': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] 248 | EdgeSet ProcessComponent(const VertexSet &reached, | ~~~~~~~~~~~~~~~~~^~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const Graph&, const std::set, std::allocator >&, size_t)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 275 | for (EdgeId e : annotated) { | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const Graph&, const EdgeSet&, size_t, double, double, const string&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 465 | for (EdgeId e : annotated) { | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 97%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp [ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/read_corrector.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const string&, const string&, size_t)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ [ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/hammer/expander.cpp [ 97%] Linking CXX executable ../../bin/spaligner cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so [ 97%] Linking CXX executable ../../bin/unitig-coverage cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target spaligner [ 98%] Linking CXX executable ../../bin/spades-hammer cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so [ 98%] Linking CXX executable ../../bin/form_truealignments cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/form_truealignments ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target unitig-coverage make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-hammer make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target form_truealignments In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/toolchain/utils.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 98%] Linking CXX executable ../../bin/cds-mapping-stats cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-mapping-stats.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-mapping-stats.dir/stats.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-mapping-stats ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target cds-mapping-stats [100%] Linking CXX executable ../../bin/cds-subgraphs cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-subgraphs In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [100%] Linking CXX executable ../../bin/mag-improve cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/cmake -E cmake_link_script CMakeFiles/mag-improve.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/mag-improve.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/mag-improve ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [100%] Built target mag-improve [100%] Linking CXX executable ../../bin/spades-gsimplifier cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gsimplifier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o" "CMakeFiles/spades-gsimplifier.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gsimplifier ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [100%] Built target spades-gsimplifier make[3]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 debruijn_test make[3]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -B/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/CMakeFiles 42 make -f CMakeFiles/Makefile2 test/debruijn/CMakeFiles/debruijn_test.dir/all make[4]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/coverage_model /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake --color= make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target coverage_model Consolidate compiler generated dependencies of target mimalloc-obj make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/cppformat /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/llvm /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/gqf /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/edlib /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake --color= make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake --color= Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target edlib Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target gqf make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/compiler_depend.internal". make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target format Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target version make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target gtest Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 2%] Built target mimalloc-obj Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target binary_io Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". [ 4%] Built target edlib Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target coverage_model Consolidate compiler generated dependencies of target BamTools make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 7%] Built target gqf [ 7%] Built target gtest make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend [ 9%] Built target format [ 11%] Built target version make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend [ 11%] Built target binary_io make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/teamcity_gtest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake --color= make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend [ 30%] Built target BamTools make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target llvm-support Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target teamcity_gtest make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target sequence Consolidate compiler generated dependencies of target paired_info make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target utils make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". [ 30%] Built target teamcity_gtest make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/faidx.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kstring.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target samtools [ 33%] Built target sequence make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 35%] Built target utils [ 35%] Built target paired_info [ 57%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= [ 64%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/parser.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/sam/read.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target input make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target assembly_graph [ 69%] Built target input make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 73%] 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[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target modules make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 78%] Built target modules make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target pipeline make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 90%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= Dependencies file "common/stages/CMakeFiles/stages.dir/construction.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/simplification.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target stages make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 92%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake --color= Dependencies file "common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o.d" is newer than depends file "/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target common_modules make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/CMakeFiles/common_modules.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 92%] Built target common_modules make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn/CMakeFiles/debruijn_test.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src 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/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 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test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o -MF CMakeFiles/debruijn_test.dir/construction_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/construction_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/construction_test.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::RawPoint&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp:24:12: warning: unused variable 'read_count' [-Wunused-variable] 24 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::Point&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp:31:12: warning: unused variable 'read_count' [-Wunused-variable] 31 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, | ^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadGraph(const string&, debruijn_graph::Graph&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp:70:26: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 70 | VertexId new_id = graph.AddVertex(typename Graph::VertexData(), vid, conj_vid); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp:128:24: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 128 | EdgeId new_id = graph.AddEdge(start_id, fin_id, Graph::EdgeData(tmp), eid, conj_eid); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadPositions(const string&, omnigraph::EdgesPositionHandler&)': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp:193:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] 193 | int read_count = fscanf(file, "%zu\n", &pos_count); | ^~~~~~~~~~ [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:84:57: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:46:38: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const debruijn_graph::config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, debruijn_graph::Graph&) [with Read = io::SingleRead; debruijn_graph::KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const debruijn_graph::config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, debruijn_graph::Graph&) [with Streams = io::ReadStreamList; debruijn_graph::KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const debruijn_graph::config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, debruijn_graph::Graph&, debruijn_graph::EdgeIndex&) [with Streams = io::ReadStreamList; debruijn_graph::KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:33:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:63:26: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:10: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(debruijn_graph::KmerMapper::EdgeId, debruijn_graph::KmerMapper::EdgeId, debruijn_graph::KmerMapper::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::KmerMapper::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graphio.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:48:62: required from 'debruijn_graph::RandomGraphAccessor::EdgeId debruijn_graph::RandomGraphAccessor::GetRandomEdge() const [with Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::RandomGraphAccessor::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:173:48: required from 'void debruijn_graph::RandomPairedIndex::RemoveRandomEdgeInfo() [with Index = omnigraph::de::PairedIndex]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:184:13: required from 'void debruijn_graph::RandomPairedIndex::PerformRandomOperation() [with Index = omnigraph::de::PairedIndex]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:176:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:40:13: required from 'debruijn_graph::RandomGraphAccessor::VertexId debruijn_graph::RandomGraphAccessor::GetRandomVertex() const [with Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::RandomGraphAccessor::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:100:51: required from 'void debruijn_graph::RandomGraph::AddRandomEdge() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:119:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:112:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, omnigraph::EdgeProcessingAlgorithm::ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgeProcessingAlgorithm::ProceedConditionT = func::TypedPredicate]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:222:72: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/test_utils.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/test_utils.cpp:125:55: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/test_utils.cpp:9: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const debruijn_graph::config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, debruijn_graph::Graph&) [with Read = io::SingleRead; debruijn_graph::KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const debruijn_graph::config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, debruijn_graph::Graph&) [with Streams = io::ReadStreamList; debruijn_graph::KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/test_utils.cpp:138:19: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(omnigraph::simplification::relative_coverage::Component::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::Component::VertexId = omnigraph::impl::VertexId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(omnigraph::simplification::relative_coverage::Component::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::Component::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::EdgeId = omnigraph::impl::EdgeId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::HandlerF, size_t, std::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' /usr/include/c++/11/ext/new_allocator.h:162:4: required from 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /usr/include/c++/11/bits/alloc_traits.h:516:17: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/11/bits/shared_ptr_base.h:1342:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' /usr/include/c++/11/bits/shared_ptr.h:409:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /usr/include/c++/11/bits/shared_ptr.h:862:14: required from 'std::shared_ptr<_Tp> std::allocate_shared(const _Alloc&, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator >; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}]' /usr/include/c++/11/bits/shared_ptr.h:878:39: required from 'std::shared_ptr<_Tp> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const debruijn::simplification::SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:312:83: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector::BulgeInfo>&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::ParallelBulgeRemover::SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:17, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+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 = omnigraph::impl::VertexId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:100:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:990:43: required from 'omnigraph::complex_br::LocalizedComponentFinder::LocalizedComponentFinder(const Graph&, size_t, size_t, omnigraph::complex_br::LocalizedComponentFinder::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; omnigraph::complex_br::LocalizedComponentFinder::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1059:41: required from 'bool omnigraph::complex_br::CandidateFinder::Check(omnigraph::complex_br::CandidateFinder::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::CandidateFinder::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1057:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:43:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 43 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(omnigraph::complex_br::ComplexBulgeRemover::VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(omnigraph::complex_br::ComplexBulgeRemover::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:777:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 777 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(omnigraph::complex_br::ComponentProjector::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComponentProjector::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:824:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(omnigraph::complex_br::ComplexBulgeRemover::VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(omnigraph::complex_br::ComplexBulgeRemover::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:793:16: warning: unused variable 'end_height' [-Wunused-variable] 793 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/test.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:822:43: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(omnigraph::complex_br::ComplexBulgeRemover::VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(omnigraph::complex_br::ComplexBulgeRemover::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComplexBulgeRemover::VertexId = omnigraph::impl::VertexId]' /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(omnigraph::complex_br::SkeletonTree::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::SkeletonTree::VertexId = omnigraph::impl::VertexId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:32: warning: unused parameter 'v' [-Wunused-parameter] 309 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, omnigraph::complex_br::SkeletonTree::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; omnigraph::complex_br::SkeletonTree::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:320:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:322:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 322 | for (EdgeId e : old_edges) { | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(omnigraph::complex_br::ComponentColoring::EdgeId, omnigraph::complex_br::ComponentColoring::EdgeId, omnigraph::complex_br::ComponentColoring::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::ComponentColoring::EdgeId = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:18: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:71: warning: unused parameter 'edge2' [-Wunused-parameter] 476 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/spades-lUTA64/spades-3.15.4+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 = omnigraph::impl::EdgeId]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:241:18: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 104 | gap_cfg.penalty_ratio = 0.1; | ^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:115:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 115 | ends_cfg.penalty_ratio = 0.1; | ^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:153:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 153 | if (g.int_id(*it) == eid_int){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:183:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 183 | if (g.int_id(*it) == eid_int){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 191 | gap_cfg.penalty_ratio = 0.1; | ^~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, omnigraph::GraphCore::EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] 565 | ++vptr; | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: while referencing 'e' 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [100%] Linking CXX executable ../../bin/debruijn_test cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/cmake -E cmake_link_script CMakeFiles/debruijn_test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o CMakeFiles/debruijn_test.dir/test_utils.cpp.o CMakeFiles/debruijn_test.dir/construction_test.cpp.o CMakeFiles/debruijn_test.dir/io_test.cpp.o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o CMakeFiles/debruijn_test.dir/graphio.cpp.o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o CMakeFiles/debruijn_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/debruijn_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/teamcity_gtest/libteamcity_gtest.a ../../lib/libgtest.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [100%] Built target debruijn_test make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory 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directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/bamtools/api /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/edlib /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu 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/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake --color= make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io/binary /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 2%] Built target edlib [ 2%] Built target coverage_model make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target format [ 26%] Built target llvm-support [ 29%] Built target gqf make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend [ 48%] Built target BamTools make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/paired_info /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= [ 51%] Built target version make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= [ 51%] Built target gtest make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/samtools /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/teamcity_gtest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake --color= [ 53%] Built target mimalloc-obj make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build [ 53%] Built target binary_io make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 53%] Built target teamcity_gtest make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 56%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend [ 63%] Built target samtools [ 63%] Built target paired_info make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/io /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= [ 65%] Built target sequence make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/assembly_graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 70%] Built target input make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 75%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules/path_extend /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/modules /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/pipeline /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= [ 90%] Built target modules make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 92%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/stages /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/CMakeFiles/common_modules.dir/build'. make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target common_modules make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/depend make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test/CMakeFiles/include_test.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/build make[5]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/quality_test.cpp [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/sequence_test.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/nucl_test.cpp cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/cyclic_hash_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/binary_test.cpp [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common -I/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/../ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/test.cpp In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:68: warning: 's2$' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:158:12: note: 's2$' was declared here 158 | Seq<7> s2("TTTTTTT"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:68: warning: 's1$' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:155:12: note: 's1$' was declared here 155 | Seq<7> s1("ACGTACT"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_ShiftLeft_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:265:54: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 265 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:26:13: note: 's$' was declared here 26 | Seq<10> s("ACGTACGTAC"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_ShiftRight_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:341:42: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 341 | res.data_[i] = (res.data_[i] << 2) | rm; | ~~~~~~~~~~~~~~^~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:39:13: note: 's$' was declared here 39 | Seq<10> s("ACGTACGTAC"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_Str_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:53:13: note: 's$' was declared here 53 | Seq<10> s("ACGTACGTAC"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_HeadAndTail_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:60:13: note: 's$' was declared here 60 | Seq<10> s("ACGTACGTAC"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:357:40: warning: 's3$' may be used uninitialized in this function [-Wmaybe-uninitialized] 357 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:140:12: note: 's3$' was declared here 140 | Seq<9> s3("ACGTACGTA"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:357:40: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 357 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:136:13: note: 's$' was declared here 136 | Seq<10> s("ACGTACGTAC"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_FromBiggerSeq_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:66:13: note: 's$' was declared here 66 | Seq<10> s("ACGTACGTAC"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:287:59: warning: '*(long unsigned int*)((char*)&s + offsetof(Seq<3, long unsigned int>,Seq<3, long unsigned int>::data_.std::array::_M_elems[0]))' may be used uninitialized in this function [-Wmaybe-uninitialized] 287 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:86:16: note: '*(long unsigned int*)((char*)&s + offsetof(Seq<3, long unsigned int>,Seq<3, long unsigned int>::data_.std::array::_M_elems[0]))' was declared here 86 | Seq<3> s("ACG"); | ^ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:83:38: warning: 's.Seq<4, unsigned char>::data_.std::array::_M_elems[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] 83 | EXPECT_EQ("ACGTC", s.pushBack('C').str()); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:287:59: warning: '*(long unsigned int*)((char*)&s + offsetof(Seq<4, long unsigned int>,Seq<4, long unsigned int>::data_.std::array::_M_elems[0]))' may be used uninitialized in this function [-Wmaybe-uninitialized] 287 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:78:16: note: '*(long unsigned int*)((char*)&s + offsetof(Seq<4, long unsigned int>,Seq<4, long unsigned int>::data_.std::array::_M_elems[0]))' was declared here 78 | Seq<4> s("ACGT"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_End_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's1$' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:114:12: note: 's1$' was declared here 114 | Seq<5> s1("ACGTA"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_Start_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's1$' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:119:12: note: 's1$' was declared here 119 | Seq<5> s1("ACGTA"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_Test16_2_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:265:54: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 265 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:150:13: note: 's$' was declared here 150 | Seq<16> s("TTTTTTTTTTTTTTTT"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void Seq_Test16_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:265:54: warning: 's$' may be used uninitialized in this function [-Wmaybe-uninitialized] 265 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/seq_test.cpp:145:13: note: 's$' was declared here 145 | Seq<16> s("AAAAAAAAAAAAAAAA"); | ^ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/rtseq.hpp:25, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: '*(long unsigned int*)((char*)&s3 + offsetof(Seq<32, long unsigned int>,Seq<32, long unsigned int>::data_.std::array::_M_elems[0]))' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:331:13: note: '*(long unsigned int*)((char*)&s3 + offsetof(Seq<32, long unsigned int>,Seq<32, long unsigned int>::data_.std::array::_M_elems[0]))' was declared here 331 | Seq<32> s3("ACGTACGTACACGTACGTACACGTACGTACAC"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/rtseq.hpp:25, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: '*(long unsigned int*)((char*)&s2 + offsetof(Seq<16, long unsigned int>,Seq<16, long unsigned int>::data_.std::array::_M_elems[0]))' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:330:13: note: '*(long unsigned int*)((char*)&s2 + offsetof(Seq<16, long unsigned int>,Seq<16, long unsigned int>::data_.std::array::_M_elems[0]))' was declared here 330 | Seq<16> s2("CCCCGTACGTACGTAC"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/rtseq.hpp:25, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: '*(long unsigned int*)((char*)&s1 + offsetof(Seq<10, long unsigned int>,Seq<10, long unsigned int>::data_.std::array::_M_elems[0]))' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:329:13: note: '*(long unsigned int*)((char*)&s1 + offsetof(Seq<10, long unsigned int>,Seq<10, long unsigned int>::data_.std::array::_M_elems[0]))' was declared here 329 | Seq<10> s1("ACGTACGTAC"); | ^~ In file included from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/rtseq.hpp:25, from /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:7: /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: '*(long unsigned int*)((char*)&s + offsetof(Seq<5, long unsigned int>,Seq<5, long unsigned int>::data_.std::array::_M_elems[0]))' may be used uninitialized in this function [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src/test/include_test/rtseq_test.cpp:328:12: note: '*(long unsigned int*)((char*)&s + offsetof(Seq<5, long unsigned int>,Seq<5, long unsigned int>::data_.std::array::_M_elems[0]))' was declared here 328 | Seq<5> s("CGTAC"); | ^ [100%] Linking CXX executable ../../bin/include_test cd /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/cmake -E cmake_link_script CMakeFiles/include_test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-lUTA64/spades-3.15.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/include_test.dir/seq_test.cpp.o CMakeFiles/include_test.dir/sequence_test.cpp.o CMakeFiles/include_test.dir/rtseq_test.cpp.o CMakeFiles/include_test.dir/quality_test.cpp.o CMakeFiles/include_test.dir/nucl_test.cpp.o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o CMakeFiles/include_test.dir/binary_test.cpp.o CMakeFiles/include_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/include_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/teamcity_gtest/libteamcity_gtest.a ../../lib/libgtest.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/llvm-13/lib/libLLVMSupport.a -lrt -ldl -lpthread -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-13/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' [100%] Built target include_test make[4]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg' dh: command-omitted: The call to "dh_auto_test -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_prep -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j10 install DESTDIR=/build/spades-lUTA64/spades-3.15.4\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/spades-lUTA64/spades-3.15.4+dfsg/assembler/src -B/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/metaspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/plasmidspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/rnaspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/metaviralspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/metaplasmidspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/rnaviralspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/coronaspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/truspades.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades_init.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/VERSION -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.gff -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.gff -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_truspades -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R1.fastq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz -- Installing: 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/build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/truspades_manual.html -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/rnaspades_manual.html -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/LICENSE -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/GPLv2.txt -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-core -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/moleculo_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/pe_params.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/debruijn/simplification.info -- Installing: 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/build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/corrector -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/configs/corrector/corrector.info -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-truseq-scfcorrection -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-kmercount -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-read-filter -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-kmer-estimating -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-convert-bin-to-fasta -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-gbuilder -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-gmapper -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spaligner -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spaligner/spaligner_config.yaml -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/spades-gsimplifier -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/cds-subgraphs -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/cds-mapping-stats -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/bin/mag-improve -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline/run_contig_breaker.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline/commands_parser.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline/support.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_storage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_parser.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/breaking_scaffolds_script.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/check_test_script.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/correction_iteration_script.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/plasmid_glue.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_contigs.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_interlaced_reads.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/compress_all.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/postprocessing_script.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/before_start_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/breaking_scaffolds_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/check_test_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/error_correction_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/pipeline.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/postprocessing_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/preprocess_reads_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/scaffold_correction_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_iteration_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/terminating_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/correction_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/__init__.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/barcode_extraction.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/generate_quality.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/id_generation.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/launch_options.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/break_by_coverage.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//common -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/SeqIO.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/__init__.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/alignment.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/parallel_launcher.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/sam_parser.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_local.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_save_yaml.py -- Installing: /build/spades-lUTA64/spades-3.15.4+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executors.py make[1]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg' # Use Debian-packaged yaml module find debian/spades \ -type f \ -exec sed -i 's/pyyaml[2|3]/yaml/' {} + mkdir -p debian/spades/usr/libexec/spades/ mv debian/spades/usr/bin/* debian/spades/usr/libexec/spades/ rm -f debian/spades/usr/share/spades/*.html rm -f debian/spades/usr/share/spades/manual.md rm -f debian/spades/usr/share/spades/GPLv2.txt rm -f debian/spades/usr/share/spades/README.md rm -f debian/spades/usr/share/spades/LICENSE make[1]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg' dh_install -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installdocs -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/spades-lUTA64/spades-3.15.4+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-lUTA64/spades-3.15.4+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/spades-lUTA64/spades-3.15.4+dfsg' mkdir -p /build/spades-lUTA64/spades-3.15.4+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/spades-lUTA64/spades-3.15.4+dfsg/debian/man_src/*.adoc cp /build/spades-lUTA64/spades-3.15.4+dfsg/debian/man_src/*.? /build/spades-lUTA64/spades-3.15.4+dfsg/debian/man dh_installman make[1]: Leaving directory '/build/spades-lUTA64/spades-3.15.4+dfsg' dh_python3 -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_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_3.15.4+dfsg-1_amd64.deb'. dpkg-deb: building package 'spades' in '../spades_3.15.4+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../spades_3.15.4+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../spades_3.15.4+dfsg-1_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-lUTA64 /tmp/spades-3.15.4+dfsg-1rim78oqn I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.Za_uUK5iUv... I: success in 2067.5544 seconds md5: spades-dbgsym_3.15.4+dfsg-1_amd64.deb: OK md5: spades_3.15.4+dfsg-1_amd64.deb: OK sha1: spades-dbgsym_3.15.4+dfsg-1_amd64.deb: OK sha1: spades_3.15.4+dfsg-1_amd64.deb: OK sha256: spades-dbgsym_3.15.4+dfsg-1_amd64.deb: OK sha256: spades_3.15.4+dfsg-1_amd64.deb: OK Checksums: OK