Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/h/hhsuite/hhsuite_3.3.0+ds-6+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/hhsuite-3.3.0+ds-6+b1ac48q8_n/hhsuite_3.3.0+ds-6+b1_amd64.buildinfo Get source package info: hhsuite=3.3.0+ds-6 Source URL: http://snapshot.notset.fr/mr/package/hhsuite/3.3.0+ds-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=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=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 cmake=3.23.1-2 cmake-data=3.23.1-2 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.1 dh-autoreconf=20 dh-elpa-helper=2.0.10 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=1:5.41-4 findutils=4.9.0-3 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 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 help2man=1.49.2 hicolor-icon-theme=0.17-2 hostname=3.23 imagemagick=8:6.9.11.60+dfsg-1.3+b2 imagemagick-6-common=8:6.9.11.60+dfsg-1.3 imagemagick-6.q16=8:6.9.11.60+dfsg-1.3+b2 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libaom3=3.3.0-1 libarchive-zip-perl=1.68-1 libarchive13=3.6.0-1 libasan6=11.3.0-1 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=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 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 libcurl4=7.83.0-1 libdav1d5=0.9.2-1+b1 libdb5.3=5.3.28+dfsg1-0.8 libde265-0=1.0.8-1 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate0=1.10-2 libdpkg-perl=1.21.7 libelf1=0.186-1 libexpat1=2.4.8-1 libffi8=3.4.2-4 libfftw3-double3=3.3.8-2 libfile-stripnondeterminism-perl=1.13.0-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.11.1+dfsg-2 libgcc-11-dev=11.3.0-1 libgcc-s1=12-20220319-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgssapi-krb5-2=1.19.2-2+b1 libheif1=1.12.0-2+b3 libhogweed6=3.7.3-1 libicu71=71.1-2 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12-20220319-1 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.1.2-1 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 liblcms2-2=2.12~rc1-2 libldap-2.5-0=2.5.11+dfsg-1 liblocale-gettext-perl=1.07-4+b2 liblqr-1-0=0.4.2-2.1 liblsan0=12-20220319-1 libltdl7=2.4.7-3 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmagickcore-6.q16-6=8:6.9.11.60+dfsg-1.3+b2 libmagickwand-6.q16-6=8:6.9.11.60+dfsg-1.3+b2 libmd0=1.0.4-1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libncurses6=6.3+20220423-1 libncursesw6=6.3+20220423-1 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma1=2.0.14-3 libopenjp2-7=2.4.0-6 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpng16-16=1.6.37-5 libprocps8=2:3.3.17-7+b1 libpsl5=0.21.0-1.2 libquadmath0=12-20220319-1 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-4 libsasl2-modules-db=2.1.28+dfsg-4 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsimde-dev=0.7.2-6 libsmartcols1=2.38-4 libssh2-1=1.10.0-3 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.3.0-1 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtiff5=4.3.0-7 libtinfo6=6.3+20220423-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-3 libtsan0=11.3.0-1 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.38-4 libuv1=1.44.1-2 libwebp7=1.2.2-2+b1 libwebpdemux2=1.2.2-2+b1 libwebpmux3=1.2.2-2+b1 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libx265-199=3.5-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.13+dfsg-1+b1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3+20220423-1 ncurses-bin=6.3+20220423-1 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 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 ucf=3.0043 util-linux=2.38-4 util-linux-extra=2.38-4 xz-utils=5.2.5-2.1 zlib1g=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/20211125T024936Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211125T024936Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220511T145217Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220428T025707Z/ 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 hhsuite=3.3.0+ds-6 && mkdir -p /build/hhsuite-GMKPav && dpkg-source --no-check -x /*.dsc /build/hhsuite-GMKPav/hhsuite-3.3.0+ds && cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds && { printf '%s' 'hhsuite (3.3.0+ds-6+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-ubc-01) Sun, 01 May 2022 20:54:22 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/hhsuite-GMKPav" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651438462" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/hhsuite-GMKPav /tmp/hhsuite-3.3.0+ds-6+b1ac48q8_n bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220428T025707Z 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.t0EYF1TPet 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.t0EYF1TPet Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). 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/20220428T025707Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220428T025707Z 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 (1118 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 ... 4627 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/20211125T024936Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211125T024936Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220511T145217Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220428T025707Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.t0EYF1TPet Get:1 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220511T145217Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220428T025707Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220511T145217Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220511T145217Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220511T145217Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220511T145217Z unstable/main amd64 Packages [12.4 MB] Fetched 35.6 MB in 29s (1247 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.t0EYF1TPet I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d hhsuite=3.3.0+ds-6 && mkdir -p /build/hhsuite-GMKPav && dpkg-source --no-check -x /*.dsc /build/hhsuite-GMKPav/hhsuite-3.3.0+ds && cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds && { printf '%s' 'hhsuite (3.3.0+ds-6+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-ubc-01) Sun, 01 May 2022 20:54:22 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/hhsuite-GMKPav"' exec /tmp/mmdebstrap.t0EYF1TPet Reading package lists... NOTICE: 'hhsuite' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hhsuite.git Please use: git clone https://salsa.debian.org/med-team/hhsuite.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4794 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main hhsuite 3.3.0+ds-6 (dsc) [2126 B] Get:2 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main hhsuite 3.3.0+ds-6 (tar) [4775 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211125T024936Z bookworm/main hhsuite 3.3.0+ds-6 (diff) [16.6 kB] Fetched 4794 kB in 4s (1292 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'hhsuite_3.3.0+ds-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting hhsuite in /build/hhsuite-GMKPav/hhsuite-3.3.0+ds dpkg-source: info: unpacking hhsuite_3.3.0+ds.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.3.0+ds-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test_without_mpi dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying perl_interpreter dpkg-source: info: applying drop-fmemopen.h.patch dpkg-source: info: applying python3 dpkg-source: info: applying ppc64el.patch dpkg-source: info: applying exe_suffix I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651438462" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.t0EYF1TPet dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-6+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_auto_clean rm -rf hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 build-* mybuild find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ dh_auto_configure --builddirectory build_${SIMD} -- -DEXE_SUFFIX=-${SIMD} -DNATIVE_ARCH=0; \ done cd build_avx2 && 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 -DEXE_SUFFIX=-avx2 -DNATIVE_ARCH=0 .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- 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 -- Compiler is GNU -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- 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 CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 cd build_avx && 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 -DEXE_SUFFIX=-avx -DNATIVE_ARCH=0 .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- 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 -- Compiler is GNU -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- 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 CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx cd build_sse4.1 && 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 -DEXE_SUFFIX=-sse4.1 -DNATIVE_ARCH=0 .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- 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 -- Compiler is GNU -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- 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 CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 cd build_ssse3 && 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 -DEXE_SUFFIX=-ssse3 -DNATIVE_ARCH=0 .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- 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 -- Compiler is GNU -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- 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 CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 cd build_sse3 && 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 -DEXE_SUFFIX=-sse3 -DNATIVE_ARCH=0 .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- 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 -- Compiler is GNU -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- 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 CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" && \ dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain -DNATIVE_ARCH=0 cd build_plain && 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 -DEXE_SUFFIX=-plain -DNATIVE_ARCH=0 .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- 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 -- Compiler is GNU -- Looking for fmemopen -- Looking for fmemopen - found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- 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 CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain make[1]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \ dh_auto_build --builddirectory build_${SIMD} ; \ done cd build_avx2 && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/CMakeFiles /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/data/CMakeFiles/generated.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 1%] Generating ../generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build [ 2%] Generating ../generated/cs219.lib.h [ 3%] Generating ../generated/context_data.crf.h make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h [ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o [ 6%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory 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-D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/aa.cc [ 7%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h [ 9%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/log.cc [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/application.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 19%] Linking C executable ffindex_apply cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 19%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src 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'/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 [ 23%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 [ 24%] Linking C executable ffindex_build /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 24%] Built target hhviterbialgorithm_with_celloff_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c [ 25%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend [ 25%] Built target ffindex_build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake --color= make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 28%] Linking C executable ffindex_from_fasta cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 [ 29%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 [ 30%] Linking C executable ffindex_modify cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 31%] Linking C executable ffindex_get cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 31%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend [ 31%] Built target ffindex_from_fasta /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color= make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color= make -f src/CMakeFiles/a3m_extract-avx2.dir/build.make src/CMakeFiles/a3m_extract-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_extract-avx2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 34%] Linking C executable ffindex_order cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a [ 35%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_extract-avx2.dir/build.make src/CMakeFiles/a3m_extract-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 36%] Building CXX object src/CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 37%] Linking C executable ffindex_unpack cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 [ 37%] Built target ffindex_get [ 37%] Built target hhviterbialgorithm_with_celloff make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_database_reduce-avx2.dir/build.make src/CMakeFiles/a3m_database_reduce-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_reduce-avx2.dir/DependInfo.cmake --color= /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_reduce-avx2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_database_reduce-avx2.dir/build.make src/CMakeFiles/a3m_database_reduce-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 37%] Built target ffindex_order make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_extract-avx2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 38%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 38%] Built target ffindex_unpack make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_database_filter-avx2.dir/DependInfo.cmake --color= [ 39%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 40%] Building CXX object src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_reduce.cpp /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 41%] Building CXX object src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 42%] Building CXX object src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 42%] Built target ffindex_from_fasta_with_split [ 43%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 43%] Built target hhviterbialgorithm_and_ss [ 44%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 44%] Built target CS_OBJECTS [ 45%] Linking CXX executable a3m_database_extract-avx2 [ 46%] Linking CXX executable a3m_database_reduce-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-avx2.dir/link.txt --verbose=1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 46%] Built target a3m_database_extract-avx2 [ 47%] Linking CXX executable a3m_extract-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o" -o a3m_extract-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 47%] Built target a3m_database_reduce-avx2 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 47%] Built target a3m_extract-avx2 [ 48%] Linking CXX executable a3m_reduce-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx2.dir/link.txt --verbose=1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 48%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 50%] Built target a3m_reduce-avx2 [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhit.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalign.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhitlist.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmatrices.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhutil.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 58%] Linking CXX executable a3m_database_filter-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 58%] Built target a3m_database_filter-avx2 [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd 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object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits-avx2.dir/build.make src/CMakeFiles/hhblits-avx2.dir/depend make -f src/CMakeFiles/hhmake-avx2.dir/build.make src/CMakeFiles/hhmake-avx2.dir/depend make -f src/CMakeFiles/hhfilter-avx2.dir/build.make src/CMakeFiles/hhfilter-avx2.dir/depend make -f src/CMakeFiles/hhsearch-avx2.dir/build.make src/CMakeFiles/hhsearch-avx2.dir/depend make -f src/CMakeFiles/hhalign-avx2.dir/build.make src/CMakeFiles/hhalign-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits-avx2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhmake-avx2.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhconsensus-avx2.dir/build.make src/CMakeFiles/hhconsensus-avx2.dir/depend make -f src/CMakeFiles/cstranslate-avx2.dir/build.make src/CMakeFiles/cstranslate-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhblits_omp-avx2.dir/build.make src/CMakeFiles/hhblits_omp-avx2.dir/depend cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhfilter-avx2.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhsearch_omp-avx2.dir/build.make src/CMakeFiles/hhsearch_omp-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhconsensus-avx2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/cstranslate-avx2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_omp-avx2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhsearch_omp-avx2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhalign_omp-avx2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhsearch-avx2.dir/build.make src/CMakeFiles/hhsearch-avx2.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhfilter-avx2.dir/build.make src/CMakeFiles/hhfilter-avx2.dir/build make -f src/CMakeFiles/hhalign-avx2.dir/build.make src/CMakeFiles/hhalign-avx2.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/cstranslate-avx2.dir/build.make src/CMakeFiles/cstranslate-avx2.dir/build make -f 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directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhconsensus-avx2.dir/build.make src/CMakeFiles/hhconsensus-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhsearch_omp-avx2.dir/build.make src/CMakeFiles/hhsearch_omp-avx2.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhalign_omp-avx2.dir/build.make src/CMakeFiles/hhalign_omp-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 81%] Building CXX object src/CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o [ 82%] Building CXX object src/CMakeFiles/hhsearch-avx2.dir/hhblits_app.cpp.o [ 83%] Building CXX object src/CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o [ 84%] Building 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CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfilter.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o -MF 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o -MF CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmake.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhconsensus.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 90%] Linking CXX executable hhsearch-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch-avx2.dir/hhblits_app.cpp.o" -o hhsearch-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 91%] Linking CXX executable hhblits-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o" -o hhblits-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 92%] Linking CXX executable hhconsensus-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o" -o hhconsensus-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 93%] Linking CXX executable hhalign-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o" -o hhalign-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 93%] Built target hhsearch-avx2 make -f src/CMakeFiles/hhblits_ca3m-avx2.dir/build.make src/CMakeFiles/hhblits_ca3m-avx2.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_ca3m-avx2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhblits_ca3m-avx2.dir/build.make src/CMakeFiles/hhblits_ca3m-avx2.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 94%] Building CXX object src/CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 95%] Linking CXX executable hhalign_omp-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 95%] Built target hhblits-avx2 [ 95%] Built target hhconsensus-avx2 [ 96%] Linking CXX executable hhfilter-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-avx2.dir/link.txt --verbose=1 [ 96%] Built target hhalign-avx2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o" -o hhfilter-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 97%] Linking CXX executable hhsearch_omp-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-avx2.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o" -o hhsearch_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 98%] Linking CXX executable hhmake-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o" -o hhmake-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 99%] Linking CXX executable hhblits_omp-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 99%] Built target hhfilter-avx2 [ 99%] Built target hhalign_omp-avx2 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 99%] Built target hhsearch_omp-avx2 [ 99%] Built target hhblits_omp-avx2 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [ 99%] Built target hhmake-avx2 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [100%] Built target hhblits_ca3m-avx2 [100%] Linking CXX executable cstranslate-avx2 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o" -o cstranslate-avx2 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' [100%] Built target cstranslate-avx2 make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd build_avx && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/CMakeFiles /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/data/CMakeFiles/generated.dir/DependInfo.cmake --color= make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 1%] Generating ../generated/context_data.crf.h [ 2%] Generating ../generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated [ 3%] Generating ../generated/cs219.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated [ 4%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated [ 6%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o [ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 7%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_compress.cpp make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h [ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 12%] Linking C static library libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 12%] Built target ffindex [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/log.cc [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/application.cc [ 17%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /usr/bin/ranlib libA3M_COMPRESS.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 19%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 21%] Linking C executable ffindex_apply cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 22%] Linking C executable ffindex_reduce cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a [ 22%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' /usr/bin/ranlib libhhviterbialgorithm_and_ss.a [ 22%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend [ 23%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake --color= [ 24%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 25%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake --color= cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend [ 28%] Linking C executable ffindex_from_fasta cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 [ 29%] Linking C executable ffindex_build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= [ 29%] Built target hhviterbialgorithm_and_ss /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color= [ 30%] Linking C executable ffindex_get make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color= [ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 34%] Linking C executable ffindex_modify cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 [ 35%] Linking C executable ffindex_unpack cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 35%] Built target ffindex_get [ 35%] Built target ffindex_build make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color= make -f src/CMakeFiles/a3m_extract-avx.dir/build.make src/CMakeFiles/a3m_extract-avx.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_extract-avx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_extract-avx.dir/build.make src/CMakeFiles/a3m_extract-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 36%] Linking C executable ffindex_order cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 [ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 38%] Building CXX object src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 38%] Built target ffindex_from_fasta make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_reduce-avx.dir/DependInfo.cmake --color= /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 39%] Building CXX object src/CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 39%] Built target hhviterbialgorithm_with_celloff_and_ss [ 39%] Built target hhviterbialgorithm_with_celloff make -f src/CMakeFiles/a3m_database_reduce-avx.dir/build.make src/CMakeFiles/a3m_database_reduce-avx.dir/depend make -f src/CMakeFiles/a3m_database_extract-avx.dir/build.make src/CMakeFiles/a3m_database_extract-avx.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_reduce-avx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_extract-avx.dir/DependInfo.cmake --color= [ 40%] Linking C executable ffindex_from_fasta_with_split [ 40%] Built target ffindex_unpack [ 40%] Built target ffindex_modify make -f src/CMakeFiles/a3m_database_filter-avx.dir/build.make src/CMakeFiles/a3m_database_filter-avx.dir/depend cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_filter-avx.dir/DependInfo.cmake --color= [ 40%] Built target ffindex_order make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_database_reduce-avx.dir/build.make src/CMakeFiles/a3m_database_reduce-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_database_filter-avx.dir/build.make src/CMakeFiles/a3m_database_filter-avx.dir/build /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_database_extract-avx.dir/build.make src/CMakeFiles/a3m_database_extract-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 42%] Building CXX object src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 43%] Building CXX object src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 44%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o [ 44%] Built target ffindex_from_fasta_with_split cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 44%] Built target generated /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 45%] Linking CXX executable a3m_extract-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o" -o a3m_extract-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 46%] Linking CXX executable a3m_reduce-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 46%] Built target a3m_extract-avx [ 46%] Built target a3m_reduce-avx [ 47%] Linking CXX executable a3m_database_extract-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 48%] Linking CXX executable a3m_database_reduce-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 48%] Built target a3m_database_reduce-avx [ 48%] Built target a3m_database_extract-avx [ 48%] Built target CS_OBJECTS make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 49%] Linking CXX executable a3m_database_filter-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-avx.dir/link.txt --verbose=1 [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalign.cpp [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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-MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o 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CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhutil.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 58%] Built target a3m_database_filter-avx [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o 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make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhalign-avx.dir/DependInfo.cmake --color= make -f src/CMakeFiles/cstranslate-avx.dir/build.make src/CMakeFiles/cstranslate-avx.dir/depend make -f src/CMakeFiles/hhblits_omp-avx.dir/build.make src/CMakeFiles/hhblits_omp-avx.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhalign_omp-avx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhfilter-avx.dir/build.make src/CMakeFiles/hhfilter-avx.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhmake-avx.dir/build.make src/CMakeFiles/hhmake-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhsearch-avx.dir/build.make src/CMakeFiles/hhsearch-avx.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhblits-avx.dir/build.make src/CMakeFiles/hhblits-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhalign-avx.dir/build.make src/CMakeFiles/hhalign-avx.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhconsensus-avx.dir/build.make src/CMakeFiles/hhconsensus-avx.dir/build [ 80%] Building CXX object src/CMakeFiles/hhmake-avx.dir/hhmake.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake-avx.dir/hhmake.cpp.o -MF CMakeFiles/hhmake-avx.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake-avx.dir/hhmake.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmake.cpp make[4]: Entering 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-include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 84%] Building CXX object src/CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhblits_omp-avx.dir/build.make src/CMakeFiles/hhblits_omp-avx.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfilter.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhconsensus.cpp make -f src/CMakeFiles/hhsearch_omp-avx.dir/build.make src/CMakeFiles/hhsearch_omp-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhalign_omp-avx.dir/build.make src/CMakeFiles/hhalign_omp-avx.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 85%] Building CXX object src/CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 86%] Building CXX object src/CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 87%] Building CXX object src/CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o [ 88%] Building CXX object src/CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 89%] Building CXX object src/CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 90%] Linking CXX executable hhalign_omp-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 91%] Linking CXX executable hhconsensus-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx.dir/link.txt --verbose=1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o" -o hhconsensus-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 92%] Linking CXX executable hhblits-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o" -o hhblits-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 92%] Built target hhconsensus-avx make -f src/CMakeFiles/hhblits_ca3m-avx.dir/build.make src/CMakeFiles/hhblits_ca3m-avx.dir/depend [ 93%] Linking CXX executable hhblits_omp-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits_ca3m-avx.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 94%] Linking CXX executable hhfilter-avx make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhblits_ca3m-avx.dir/build.make src/CMakeFiles/hhblits_ca3m-avx.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-avx.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o" -o hhfilter-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 96%] Linking CXX executable hhsearch-avx [ 95%] Linking CXX executable hhmake-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-avx.dir/link.txt --verbose=1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx.dir/link.txt --verbose=1 [ 97%] Building CXX object src/CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhmake-avx.dir/hhmake.cpp.o" -o hhmake-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o" -o hhsearch-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 98%] Linking CXX executable hhalign-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o" -o hhalign-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 98%] Built target hhfilter-avx [ 98%] Built target hhblits_omp-avx make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 98%] Built target hhblits-avx [ 98%] Built target hhsearch-avx make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 98%] Built target hhalign_omp-avx make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 98%] Built target hhmake-avx make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 98%] Built target hhalign-avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 99%] Linking CXX executable hhsearch_omp-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o" -o hhsearch_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [ 99%] Built target hhsearch_omp-avx /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [100%] Built target hhblits_ca3m-avx [100%] Linking CXX executable cstranslate-avx cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-avx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o" -o cstranslate-avx libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' [100%] Built target cstranslate-avx make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd build_sse4.1 && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/CMakeFiles /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/data/CMakeFiles/generated.dir/DependInfo.cmake --color= make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 1%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 8%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 8%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/as.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_compress.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h [ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 11%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 12%] Linking C static library libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 14%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/log.cc /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a [ 16%] Built target ffindex make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 17%] Linking CXX static library libhhviterbialgorithm_and_ss.a [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/application.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o [ 19%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o [ 19%] Built target hhviterbialgorithm_with_celloff_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build [ 20%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /usr/bin/ranlib libhhviterbialgorithm_and_ss.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 22%] Linking C executable ffindex_apply cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake --color= /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c /usr/bin/ranlib libA3M_COMPRESS.a [ 24%] Linking C executable ffindex_reduce cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 24%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build [ 24%] Built target ffindex_reduce make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 24%] Built target hhviterbialgorithm_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake --color= [ 24%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color= [ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make 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--verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 36%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c [ 37%] Linking C executable ffindex_unpack cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a [ 37%] Built target hhviterbialgorithm_with_celloff make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_extract-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_extract-sse4.1.dir/DependInfo.cmake --color= [ 37%] Built target ffindex_from_fasta make -f src/CMakeFiles/a3m_reduce-sse4.1.dir/build.make 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_database_reduce-sse4.1.dir/DependInfo.cmake --color= make -f src/CMakeFiles/a3m_database_filter-sse4.1.dir/build.make src/CMakeFiles/a3m_database_filter-sse4.1.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make -f src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_database_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_database_extract-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 39%] Building CXX object src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 40%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o [ 41%] Building CXX object src/CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 42%] Building CXX object src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_extract.cpp [ 42%] Built target ffindex_unpack [ 42%] Built target ffindex_order [ 43%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script 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CMakeFiles/CS_OBJECTS.dir/application.cc.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 44%] Built target ffindex_from_fasta_with_split cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp /usr/bin/ranlib libCS_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 45%] Linking CXX executable a3m_reduce-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-sse4.1.dir/link.txt --verbose=1 [ 46%] Linking CXX executable a3m_extract-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o" -o a3m_reduce-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o" -o a3m_extract-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 46%] Built target generated make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 47%] Linking CXX executable a3m_database_extract-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-sse4.1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 48%] Linking CXX executable a3m_database_reduce-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 49%] Linking CXX executable a3m_database_filter-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 49%] Built target a3m_extract-sse4.1 [ 49%] Built target a3m_reduce-sse4.1 [ 49%] Built target a3m_database_extract-sse4.1 [ 49%] Built target a3m_database_reduce-sse4.1 [ 49%] Built target a3m_database_filter-sse4.1 [ 49%] Built target CS_OBJECTS make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd 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object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o 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CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalign.cpp [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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-D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhprefilter.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd 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object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o 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CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits-sse4.1.dir/build.make src/CMakeFiles/hhblits-sse4.1.dir/depend make -f 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src/CMakeFiles/hhconsensus-sse4.1.dir/depend cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch-sse4.1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhalign-sse4.1.dir/DependInfo.cmake --color= make -f 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/cstranslate-sse4.1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits_omp-sse4.1.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhalign_omp-sse4.1.dir/build.make src/CMakeFiles/hhalign_omp-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhalign_omp-sse4.1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhfilter-sse4.1.dir/build.make src/CMakeFiles/hhfilter-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch-sse4.1.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-sse4.1.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch-sse4.1.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/cstranslate-sse4.1.dir/build.make src/CMakeFiles/cstranslate-sse4.1.dir/build make[4]: Leaving 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'/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 85%] Building CXX object src/CMakeFiles/hhmake-sse4.1.dir/hhmake.cpp.o [ 86%] Building CXX object src/CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake-sse4.1.dir/hhmake.cpp.o -MF CMakeFiles/hhmake-sse4.1.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake-sse4.1.dir/hhmake.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmake.cpp [ 87%] Building CXX object src/CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 88%] Building CXX object src/CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 89%] Building CXX object src/CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 90%] Linking CXX executable hhsearch-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch-sse4.1.dir/hhblits_app.cpp.o" -o hhsearch-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 91%] Linking CXX executable hhalign_omp-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhalign_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 91%] Built target hhalign_omp-sse4.1 make -f src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build.make src/CMakeFiles/hhblits_ca3m-sse4.1.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits_ca3m-sse4.1.dir/DependInfo.cmake --color= [ 92%] Linking CXX executable hhblits_omp-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-sse4.1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build.make src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 93%] Building CXX object src/CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 93%] Built target hhsearch-sse4.1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 93%] Built target hhblits_omp-sse4.1 [ 94%] Linking CXX executable hhalign-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o" -o hhalign-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable hhsearch_omp-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhsearch_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 95%] Built target hhalign-sse4.1 [ 96%] Linking CXX executable hhmake-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhmake-sse4.1.dir/hhmake.cpp.o" -o hhmake-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 97%] Linking CXX executable hhfilter-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-sse4.1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhfilter-sse4.1.dir/hhfilter.cpp.o" -o hhfilter-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 97%] Built target hhsearch_omp-sse4.1 [ 98%] Linking CXX executable hhblits-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o" -o hhblits-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 98%] Built target hhfilter-sse4.1 [ 98%] Built target hhmake-sse4.1 [ 99%] Linking CXX executable hhconsensus-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o" -o hhconsensus-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 99%] Built target hhblits-sse4.1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' [ 99%] Built target hhconsensus-sse4.1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-sse4.1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory 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lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/data/CMakeFiles/generated.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 1%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 4%] Generating ../generated/context_data.crf.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated [ 5%] Generating ../generated/context_data.lib.h [ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h [ 7%] Generating ../generated/cs219.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h [ 7%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_compress.cpp [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h [ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/as.cc [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 12%] Linking C static library libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 12%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 13%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc [ 16%] Linking C executable ffindex_apply cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/log.cc [ 17%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 19%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake [ 20%] Linking CXX static library libhhviterbialgorithm_and_ss.a [ 21%] Linking C executable ffindex_reduce cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && 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make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 21%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color= [ 22%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c [ 24%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a [ 24%] Built target hhviterbialgorithm_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a [ 27%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 29%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= [ 29%] Built target ffindex_from_fasta make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build [ 29%] Built target ffindex_build [ 29%] Built target hhviterbialgorithm_with_celloff_and_ss make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color= make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds 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/usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c [ 31%] Linking C executable ffindex_get cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build [ 31%] Built target hhviterbialgorithm_with_celloff make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h.tmp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_extract-ssse3.dir/build.make src/CMakeFiles/a3m_extract-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_extract-ssse3.dir/DependInfo.cmake --color= [ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_extract-ssse3.dir/build.make src/CMakeFiles/a3m_extract-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 35%] Linking C executable ffindex_modify cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 [ 36%] Building CXX object src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_extract.cpp /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h make -f src/CMakeFiles/a3m_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_reduce-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_reduce-ssse3.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_reduce-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 37%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 38%] Building CXX object src/CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_reduce.cpp /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a [ 39%] Linking C executable ffindex_order [ 40%] Linking C executable ffindex_unpack cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 40%] Built target ffindex_modify [ 40%] Built target ffindex_get make -f src/CMakeFiles/a3m_database_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_database_reduce-ssse3.dir/depend make -f src/CMakeFiles/a3m_database_extract-ssse3.dir/build.make src/CMakeFiles/a3m_database_extract-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_reduce-ssse3.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_extract-ssse3.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_database_extract-ssse3.dir/build.make src/CMakeFiles/a3m_database_extract-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_database_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_database_reduce-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 42%] Building CXX object src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 42%] Built target ffindex_from_fasta_with_split [ 42%] Built target ffindex_unpack [ 42%] Built target ffindex_order make -f src/CMakeFiles/a3m_database_filter-ssse3.dir/build.make src/CMakeFiles/a3m_database_filter-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_filter-ssse3.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/a3m_database_filter-ssse3.dir/build.make src/CMakeFiles/a3m_database_filter-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 43%] Building CXX object src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 44%] Linking CXX executable a3m_database_reduce-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 45%] Linking CXX executable a3m_extract-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o" -o a3m_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 45%] Built target a3m_extract-ssse3 [ 46%] Linking CXX executable a3m_reduce-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o" -o a3m_reduce-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 46%] Built target generated make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 46%] Built target a3m_reduce-ssse3 [ 46%] Built target a3m_database_reduce-ssse3 [ 47%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a [ 48%] Linking CXX executable a3m_database_extract-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 48%] Built target CS_OBJECTS make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.cpp [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhdecl.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhit.cpp [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmatrices.cpp [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalign.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhitlist.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 56%] Built target a3m_database_extract-ssse3 [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhutil.cpp [ 58%] Linking CXX executable a3m_database_filter-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF 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src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhprefilter.cpp [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhconsensus-ssse3.dir/DependInfo.cmake --color= make -f src/CMakeFiles/cstranslate-ssse3.dir/build.make src/CMakeFiles/cstranslate-ssse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhblits_omp-ssse3.dir/build.make src/CMakeFiles/hhblits_omp-ssse3.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds 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src/CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o -MF 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90%] Linking CXX executable hhblits-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits-ssse3.dir/hhblits_app.cpp.o" -o hhblits-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 91%] Linking CXX executable hhalign-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o" -o hhalign-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 91%] Built target hhalign-ssse3 make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/depend [ 91%] Built target hhblits-ssse3 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits_ca3m-ssse3.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 92%] Building CXX object src/CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 93%] Linking CXX executable hhalign_omp-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhalign_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 93%] Built target hhalign_omp-ssse3 [ 94%] Linking CXX executable hhsearch-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-ssse3.dir/link.txt --verbose=1 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch-ssse3.dir/hhblits_app.cpp.o" -o hhsearch-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 95%] Linking CXX executable hhsearch_omp-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhsearch_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 96%] Linking CXX executable hhconsensus-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o" -o hhconsensus-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 96%] Built target hhsearch-ssse3 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 96%] Built target hhconsensus-ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 96%] Built target hhsearch_omp-ssse3 [ 97%] Linking CXX executable hhmake-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhmake-ssse3.dir/hhmake.cpp.o" -o hhmake-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 98%] Linking CXX executable hhfilter-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-ssse3.dir/link.txt --verbose=1 [ 99%] Linking CXX executable hhblits_omp-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o" -o hhfilter-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 99%] Built target hhmake-ssse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [ 99%] Built target hhblits_omp-ssse3 [ 99%] Built target hhfilter-ssse3 [100%] Linking CXX executable hhblits_ca3m-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target hhblits_ca3m-ssse3 [100%] Linking CXX executable cstranslate-ssse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o" -o cstranslate-ssse3 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target cstranslate-ssse3 make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd build_sse3 && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/CMakeFiles /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/data/CMakeFiles/generated.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= [ 1%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 2%] Generating ../generated/cs219.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated [ 3%] Generating ../generated/context_data.crf.h [ 4%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o [ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color= cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c [ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 7%] Generating ../generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/aa.cc [ 9%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_compress.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h [ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/as.cc [ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 12%] Linking C static library libffindex.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 12%] Built target ffindex [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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-MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/log.cc make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 16%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld [ 17%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake [ 18%] Linking C executable ffindex_apply cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 19%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o [ 19%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend /usr/bin/ranlib libhhviterbialgorithm_and_ss.a /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a [ 20%] Linking CXX static library libA3M_COMPRESS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake --color= cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c [ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/application.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp [ 23%] Linking C executable ffindex_reduce cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend [ 24%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src 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libhhviterbialgorithm_with_celloff.a [ 24%] Built target hhviterbialgorithm_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /usr/bin/ranlib libA3M_COMPRESS.a make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 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'/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: 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lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c [ 28%] Built target hhviterbialgorithm_with_celloff_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend [ 28%] Built target A3M_COMPRESS [ 28%] Built target hhviterbialgorithm_with_celloff make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a [ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 34%] Built target ffindex_get make -f src/CMakeFiles/a3m_extract-sse3.dir/build.make src/CMakeFiles/a3m_extract-sse3.dir/depend /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && 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-Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 36%] Building CXX object src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_extract.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 37%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 [ 38%] Linking C executable ffindex_unpack cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp [ 38%] Built target ffindex_from_fasta [ 38%] Built target ffindex_modify make -f src/CMakeFiles/a3m_reduce-sse3.dir/build.make src/CMakeFiles/a3m_reduce-sse3.dir/depend [ 38%] Built target ffindex_build [ 38%] Built target ffindex_unpack make -f src/CMakeFiles/a3m_database_reduce-sse3.dir/build.make src/CMakeFiles/a3m_database_reduce-sse3.dir/depend [ 38%] Built target ffindex_from_fasta_with_split make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_reduce-sse3.dir/DependInfo.cmake --color= [ 39%] Linking C executable ffindex_order cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 make -f src/CMakeFiles/a3m_database_extract-sse3.dir/build.make src/CMakeFiles/a3m_database_extract-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_reduce-sse3.dir/DependInfo.cmake --color= /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_reduce-sse3.dir/build.make src/CMakeFiles/a3m_reduce-sse3.dir/build make -f src/CMakeFiles/a3m_database_filter-sse3.dir/build.make src/CMakeFiles/a3m_database_filter-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_extract-sse3.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_database_reduce-sse3.dir/build.make src/CMakeFiles/a3m_database_reduce-sse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/a3m_database_filter-sse3.dir/DependInfo.cmake --color= [ 40%] Building CXX object src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_database_extract-sse3.dir/build.make src/CMakeFiles/a3m_database_extract-sse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/a3m_database_filter-sse3.dir/build.make src/CMakeFiles/a3m_database_filter-sse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o [ 42%] Building CXX object src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp [ 42%] Built target ffindex_order [ 43%] Building CXX object src/CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 43%] Built target generated [ 44%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a [ 45%] Linking CXX executable a3m_extract-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o" -o a3m_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 45%] Built target CS_OBJECTS make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 46%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.cpp [ 47%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhdecl.cpp [ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhit.cpp [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.cpp [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmatrices.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 51%] Linking CXX executable a3m_reduce-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o" -o a3m_reduce-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 52%] Linking CXX executable a3m_database_extract-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 52%] Built target a3m_extract-sse3 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 53%] Linking CXX executable a3m_database_reduce-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-sse3.dir/link.txt --verbose=1 [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalign.cpp [ 54%] Built target a3m_reduce-sse3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhitlist.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 55%] Built target a3m_database_extract-sse3 [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 56%] Built target a3m_database_reduce-sse3 [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhutil.cpp [ 58%] Linking CXX executable a3m_database_filter-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/util.cpp make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 60%] Built target a3m_database_filter-sse3 [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char 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stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o 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src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o 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'/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/cstranslate-sse3.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhblits_omp-sse3.dir/build.make src/CMakeFiles/hhblits_omp-sse3.dir/depend make -f src/CMakeFiles/hhsearch_omp-sse3.dir/build.make src/CMakeFiles/hhsearch_omp-sse3.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits_omp-sse3.dir/DependInfo.cmake --color= make -f src/CMakeFiles/hhalign_omp-sse3.dir/build.make src/CMakeFiles/hhalign_omp-sse3.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhblits-sse3.dir/build.make src/CMakeFiles/hhblits-sse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhalign_omp-sse3.dir/DependInfo.cmake --color= 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake-sse3.dir/hhmake.cpp.o -MF CMakeFiles/hhmake-sse3.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake-sse3.dir/hhmake.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhmake.cpp [ 83%] Building CXX object src/CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfilter.cpp [ 84%] Building CXX object src/CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o [ 85%] Building CXX object src/CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 86%] Building CXX object src/CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhsearch_omp-sse3.dir/build.make src/CMakeFiles/hhsearch_omp-sse3.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_app.cpp [ 87%] Building CXX object src/CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 88%] Building CXX object src/CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhconsensus.cpp [ 89%] Building CXX object src/CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 90%] Linking CXX executable hhalign-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o" -o hhalign-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 91%] Linking CXX executable hhsearch-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-sse3.dir/link.txt --verbose=1 [ 92%] Linking CXX executable hhblits-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits-sse3.dir/hhblits_app.cpp.o" -o hhblits-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o" -o hhsearch-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 93%] Linking CXX executable hhalign_omp-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o" -o hhalign_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 93%] Built target hhalign-sse3 make -f src/CMakeFiles/hhblits_ca3m-sse3.dir/build.make src/CMakeFiles/hhblits_ca3m-sse3.dir/depend [ 93%] Built target hhblits-sse3 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits_ca3m-sse3.dir/DependInfo.cmake --color= [ 93%] Built target hhsearch-sse3 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhblits_ca3m-sse3.dir/build.make src/CMakeFiles/hhblits_ca3m-sse3.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 94%] Building CXX object src/CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp [ 95%] Linking CXX executable hhsearch_omp-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o" -o hhsearch_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 96%] Linking CXX executable hhmake-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-sse3.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhmake-sse3.dir/hhmake.cpp.o" -o hhmake-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 96%] Built target hhalign_omp-sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 97%] Linking CXX executable hhfilter-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o" -o hhfilter-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 98%] Linking CXX executable hhblits_omp-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 98%] Built target hhmake-sse3 [ 98%] Built target hhsearch_omp-sse3 [ 98%] Built target hhfilter-sse3 [ 99%] Linking CXX executable hhconsensus-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-sse3.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o" -o hhconsensus-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [ 99%] Built target hhblits_omp-sse3 [ 99%] Built target hhconsensus-sse3 /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [100%] Built target hhblits_ca3m-sse3 [100%] Linking CXX executable cstranslate-sse3 cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o" -o cstranslate-sse3 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' [100%] Built target cstranslate-sse3 make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd build_plain && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/CMakeFiles /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/data /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/data/CMakeFiles/generated.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 1%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o [ 2%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 3%] Generating ../generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 4%] Generating ../generated/cs219.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated [ 5%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/as.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h [ 6%] Generating ../generated/context_data.crf.h cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h [ 7%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h [ 8%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp [ 10%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs/log.cc [ 15%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); | ~~~^ ~~~~~~~~~~~ | | | | long long int int64_t {aka long int} | %ld /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o [ 20%] Linking C executable ffindex_apply cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake --color= [ 22%] Built target 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-I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 [ 32%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend [ 32%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 32%] Built target ffindex_build [ 32%] Built target ffindex_get [ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c [ 34%] Linking C executable ffindex_unpack cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h > /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color= /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 35%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c [ 35%] Built target ffindex_unpack make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /usr/bin/ranlib libA3M_COMPRESS.a [ 36%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h.tmp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 36%] Built target generated [ 36%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/depend make -f src/CMakeFiles/a3m_reduce-plain.dir/build.make src/CMakeFiles/a3m_reduce-plain.dir/depend make -f src/CMakeFiles/a3m_database_reduce-plain.dir/build.make src/CMakeFiles/a3m_database_reduce-plain.dir/depend make -f src/CMakeFiles/a3m_database_extract-plain.dir/build.make src/CMakeFiles/a3m_database_extract-plain.dir/depend make -f src/CMakeFiles/a3m_database_filter-plain.dir/build.make src/CMakeFiles/a3m_database_filter-plain.dir/depend [ 37%] Linking CXX static library libCS_OBJECTS.a cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake [ 38%] Linking C executable ffindex_order cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_reduce-plain.dir/DependInfo.cmake --color= cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_database_reduce-plain.dir/DependInfo.cmake --color= make -f src/CMakeFiles/a3m_reduce-plain.dir/build.make src/CMakeFiles/a3m_reduce-plain.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 39%] Linking C executable ffindex_from_fasta_with_split cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 [ 40%] Building CXX object src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_reduce.cpp /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_extract-plain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/a3m_database_reduce-plain.dir/build.make src/CMakeFiles/a3m_database_reduce-plain.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o.d -o 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Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 42%] Building CXX object src/CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp [ 43%] Building CXX object src/CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_extract.cpp make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_database_extract-plain.dir/DependInfo.cmake --color= [ 43%] Built target ffindex_order [ 43%] Built target ffindex_from_fasta_with_split make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/a3m_database_extract-plain.dir/build.make src/CMakeFiles/a3m_database_extract-plain.dir/build make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 44%] Building CXX object src/CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp /usr/bin/ranlib libCS_OBJECTS.a [ 45%] Linking CXX executable a3m_reduce-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro 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src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c 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/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF 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src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.h:6, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhviterbi.cpp [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src 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Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 87%] Building CXX object src/CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o -MF 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-fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 89%] Building CXX object src/CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp [ 90%] Linking CXX executable hhblits-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-plain.dir/link.txt --verbose=1 [ 91%] Linking CXX executable hhsearch-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits-plain.dir/hhblits_app.cpp.o" -o hhblits-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch-plain.dir/hhblits_app.cpp.o" -o hhsearch-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 92%] Linking CXX executable hhconsensus-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-plain.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhconsensus-plain.dir/hhconsensus.cpp.o" -o hhconsensus-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 92%] Built target hhblits-plain make -f src/CMakeFiles/hhblits_ca3m-plain.dir/build.make src/CMakeFiles/hhblits_ca3m-plain.dir/depend [ 92%] Built target hhsearch-plain make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-GMKPav/hhsuite-3.3.0+ds /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhblits_ca3m-plain.dir/DependInfo.cmake --color= [ 93%] Linking CXX executable hhalign_omp-plain make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/hhblits_ca3m-plain.dir/build.make src/CMakeFiles/hhblits_ca3m-plain.dir/build cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-plain.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 94%] Building CXX object src/CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/generated -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src -I/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o" -o hhalign_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 95%] Linking CXX executable hhsearch_omp-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-plain.dir/link.txt --verbose=1 [ 96%] Linking CXX executable hhfilter-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-plain.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 97%] Linking CXX executable hhmake-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-plain.dir/link.txt --verbose=1 [ 98%] Linking CXX executable hhalign-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o" -o hhsearch_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhalign-plain.dir/hhblits_app.cpp.o" -o hhalign-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhmake-plain.dir/hhmake.cpp.o" -o hhmake-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhfilter-plain.dir/hhfilter.cpp.o" -o hhfilter-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 98%] Built target hhconsensus-plain make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhsearch.h:34, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 98%] Built target hhalign_omp-plain make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 98%] Built target hhfilter-plain [ 98%] Built target hhmake-plain make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 99%] Linking CXX executable hhblits_omp-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-plain.dir/link.txt --verbose=1 [ 99%] Built target hhsearch_omp-plain make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o" -o hhblits_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 99%] Built target hhalign-plain make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [ 99%] Built target hhblits_omp-plain /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); | ^~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/11/cstdio:42, from /usr/include/c++/11/ext/string_conversions.h:43, from /usr/include/c++/11/bits/basic_string.h:6608, from /usr/include/c++/11/string:55, from /usr/include/c++/11/bits/locale_classes.h:40, from /usr/include/c++/11/bits/ios_base.h:41, from /usr/include/c++/11/ios:42, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits.h:11, from /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable hhblits_ca3m-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [100%] Built target hhblits_ca3m-plain [100%] Linking CXX executable cstranslate-plain cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-GMKPav/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o" -o cstranslate-plain libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' [100%] Built target cstranslate-plain make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -E cmake_progress_start /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain/CMakeFiles 0 make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[1]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \ dh_auto_install --builddirectory build_${SIMD} ; \ done cd build_avx2 && make -j10 install DESTDIR=/build/hhsuite-GMKPav/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-avx2 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx2' cd build_avx && make -j10 install DESTDIR=/build/hhsuite-GMKPav/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-avx -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-avx -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_avx' cd build_sse4.1 && make -j10 install DESTDIR=/build/hhsuite-GMKPav/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-sse4.1 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-sse4.1 -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse4.1' cd build_ssse3 && make -j10 install DESTDIR=/build/hhsuite-GMKPav/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-ssse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-ssse3 -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_ssse3' cd build_sse3 && make -j10 install DESTDIR=/build/hhsuite-GMKPav/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-sse3 -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-sse3 -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_sse3' cd build_plain && make -j10 install DESTDIR=/build/hhsuite-GMKPav/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/hhsuite-GMKPav/hhsuite-3.3.0+ds -B/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp-plain -- Installing: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m-plain -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds/build_plain' mkdir -p /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/hhsuite/usr/bin dh_install -phhsuite debian/bin/simd-dispatch /usr/libexec/hhsuite/ for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter cstranslate ; do dh_install usr/bin/${prog}* /usr/libexec/hhsuite/; done cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/hhsuite/usr/bin \ && for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter; do \ ln -s ../libexec/hhsuite/simd-dispatch ${prog} ; done cd /build/hhsuite-GMKPav/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin \ && for prog in cstranslate ; do \ ln -s ../simd-dispatch ${prog} ; done dh_install -phhsuite usr/bin/ffindex_* usr/bin/ make[1]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman-arch make[1]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/hhsuite/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits" 'debian/hhsuite/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits_omp" 'debian/hhsuite/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhconsensus" 'debian/hhsuite/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhfilter" 'debian/hhsuite/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhmake" 'debian/hhsuite/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1' export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhsearch" 'debian/hhsuite/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman --arch make[1]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_fixperms chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm make[1]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-6), " make[1]: Leaving directory '/build/hhsuite-GMKPav/hhsuite-3.3.0+ds' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-6+b1_amd64.deb'. dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-6+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../hhsuite_3.3.0+ds-6+b1_amd64.buildinfo dpkg-genchanges --build=any -O../hhsuite_3.3.0+ds-6+b1_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/hhsuite-GMKPav /tmp/hhsuite-3.3.0+ds-6+b1ac48q8_n I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.t0EYF1TPet... I: success in 1378.1409 seconds md5: hhsuite-dbgsym_3.3.0+ds-6+b1_amd64.deb: OK md5: Value of 'md5' differs for hhsuite_3.3.0+ds-6+b1_amd64.deb md5: Size differs for hhsuite_3.3.0+ds-6+b1_amd64.deb sha1: hhsuite-dbgsym_3.3.0+ds-6+b1_amd64.deb: OK sha1: Value of 'sha1' differs for hhsuite_3.3.0+ds-6+b1_amd64.deb sha1: Size differs for hhsuite_3.3.0+ds-6+b1_amd64.deb sha256: hhsuite-dbgsym_3.3.0+ds-6+b1_amd64.deb: OK sha256: Value of 'sha256' differs for hhsuite_3.3.0+ds-6+b1_amd64.deb sha256: Size differs for hhsuite_3.3.0+ds-6+b1_amd64.deb Checksums: FAIL Cannot generate diffoscope for hhsuite_3.3.0+ds-6+b1_amd64.deb: RetryError[]