Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/h/hyphy/hyphy_2.5.36+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/hyphy-2.5.36+dfsg-1pwyew7dt/hyphy_2.5.36+dfsg-1_amd64.buildinfo Get source package info: hyphy=2.5.36+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/hyphy/2.5.36+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.37.90.20220207-1 binutils-common=2.37.90.20220207-1 binutils-x86-64-linux-gnu=2.37.90.20220207-1 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 chrpath=0.16-2+b1 cmake=3.22.1-1+b1 cmake-data=3.22.1-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-16 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.6 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=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-16 gcc=4:11.2.0-2 gcc-11=11.2.0-16 gcc-11-base=11.2.0-16 gettext=0.21-4 gettext-base=0.21-4 gfortran-11=11.2.0-16 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 ibverbs-providers=39.0-1 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libarchive13=3.5.2-1 libasan6=11.2.0-16 libatomic1=11.2.0-16 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37.90.20220207-1 libblkid1=2.37.3-1+b1 libbrotli1=1.0.9-2+b3 libbsd0=0.11.5-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-5 libc-dev-bin=2.33-5 libc6=2.33-5 libc6-dev=2.33-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcbor0.8=0.8.0-2 libcc1-0=11.2.0-16 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.37.90.20220207-1 libctf0=2.37.90.20220207-1 libcurl3-gnutls=7.81.0-1 libcurl4=7.81.0-1 libcurl4-gnutls-dev=7.81.0-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.1 libedit2=3.1-20210910-1 libelf1=0.186-1 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.4.4-1 libfabric1=1.11.0-3 libffi8=3.4.2-4 libfido2-1=1.10.0-1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-16 libgcc-s1=11.2.0-16 libgcrypt20=1.9.4-5 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran-11-dev=11.2.0-16 libgfortran5=11.2.0-16 libglib2.0-0=2.70.3-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=11.2.0-16 libgpg-error0=1.43-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libhwloc-dev=2.7.0-2 libhwloc-plugins=2.7.0-2 libhwloc15=2.7.0-2 libibverbs-dev=39.0-1 libibverbs1=39.0-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-16 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui=1.13.0+dfsg-1 libjsoncpp25=1.9.5-3 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1+b1 liblsan0=11.2.0-16 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmount1=2.37.3-1+b1 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libncurses6=6.3-2 libncursesw6=6.3-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnl-3-200=3.5.0-0.1 libnl-3-dev=3.5.0-0.1 libnl-route-3-200=3.5.0-0.1 libnl-route-3-dev=3.5.0-0.1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.2-1 libopenmpi3=4.1.2-1 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpciaccess0=0.16-3 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libpmix-dev=4.1.1~rc6-1 libpmix2=4.1.1~rc6-1 libprocps8=2:3.3.17-6 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libquadmath0=11.2.0-16 librdmacm1=39.0-1 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-3 libsasl2-modules-db=2.1.27+dfsg2-3 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsemanage-common=3.3-1 libsemanage2=3.3-1+b1 libsepol2=3.3-1 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.37.2-2 libsqlite3-dev=3.37.2-2 libssh2-1=1.10.0-2 libssl-dev=1.1.1m-1 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-16 libstdc++6=11.2.0-16 libsub-override-perl=0.09-2 libsystemd0=250.3-2 libtasn1-6=4.18.0-4 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-16 libubsan1=11.2.0-16 libuchardet0=0.0.7-1 libucx0=1.12.1~rc1-1 libudev1=250.3-2 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libuv1=1.43.0-1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.12+dfsg-5+b1 libxnvctrl0=470.103.01-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.16.7-2 login=1:4.11.1+dfsg1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.1-1 mawk=1.3.4.20200120-3+b1 mpi-default-dev=1.14 ncurses-base=6.3-2 ncurses-bin=6.3-2 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.2-1 openmpi-common=4.1.2-1 openssh-client=1:8.7p1-4 passwd=1:4.11.1+dfsg1-1 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-6 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 util-linux=2.37.3-1+b1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220213T030339Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220213T030339Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220215T085155Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220209T214738Z/ 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 hyphy=2.5.36+dfsg-1 && mkdir -p /build/hyphy-fyzopI && dpkg-source --no-check -x /*.dsc /build/hyphy-fyzopI/hyphy-2.5.36+dfsg && chown -R builduser:builduser /build/hyphy-fyzopI" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1644582931" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/hyphy-fyzopI /tmp/hyphy-2.5.36+dfsg-1pwyew7dt bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220209T214738Z 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.fKOCaaQ8Ql 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.fKOCaaQ8Ql Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220209T214738Z unstable/main amd64 libfakeroot amd64 1.27-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220209T214738Z unstable/main amd64 fakeroot amd64 1.27-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (749 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 ... 4697 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.27-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.27-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.27-1_amd64.deb ... Unpacking fakeroot (1.27-1) ... Setting up libfakeroot:amd64 (1.27-1) ... Setting up fakeroot (1.27-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-5) ... 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/20220213T030339Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220213T030339Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220215T085155Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220209T214738Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.fKOCaaQ8Ql Get:1 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220215T085155Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220209T214738Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main Sources [11.8 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220215T085155Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220215T085155Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220215T085155Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220215T085155Z unstable/main amd64 Packages [12.1 MB] Fetched 35.5 MB in 29s (1203 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.fKOCaaQ8Ql I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d hyphy=2.5.36+dfsg-1 && mkdir -p /build/hyphy-fyzopI && dpkg-source --no-check -x /*.dsc /build/hyphy-fyzopI/hyphy-2.5.36+dfsg && chown -R builduser:builduser /build/hyphy-fyzopI"' exec /tmp/mmdebstrap.fKOCaaQ8Ql Reading package lists... NOTICE: 'hyphy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hyphy.git Please use: git clone https://salsa.debian.org/med-team/hyphy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2492 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main hyphy 2.5.36+dfsg-1 (dsc) [2265 B] Get:2 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main hyphy 2.5.36+dfsg-1 (tar) [2474 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220213T030339Z bookworm/main hyphy 2.5.36+dfsg-1 (diff) [16.5 kB] Fetched 2492 kB in 2s (1204 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'hyphy_2.5.36+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting hyphy in /build/hyphy-fyzopI/hyphy-2.5.36+dfsg dpkg-source: info: unpacking hyphy_2.5.36+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.5.36+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_sqlite.patch dpkg-source: info: applying rm_arch_specific_flags.patch dpkg-source: info: applying set-zlib-after-setting-default-libs.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1644582931" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.fKOCaaQ8Ql dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.5.36+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' dh_auto_clean --builddirectory obj-avx dh_auto_clean --builddirectory obj-sse3 dh_auto_clean make[1]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary-arch dh binary-arch --buildsystem=cmake dh_update_autotools_config -a -O--buildsystem=cmake dh_autoreconf -a -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -std=c++14 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.81.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.37.2 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -pthread -fopenmp -- 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 INSTALL_PREFIX -- Build files have been written to: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu dh_auto_configure --builddirectory obj-avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF cd obj-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 -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_FMA3 -- Performing Test HAVE_FMA3 - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -std=c++14 -mavx -mfma -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.81.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.37.2 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -mavx -mfma -pthread -fopenmp -- 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 INSTALL_PREFIX -- Build files have been written to: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx dh_auto_configure --builddirectory obj-sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF cd obj-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 -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -std=c++14 -msse3 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.81.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.37.2 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -msse3 -pthread -fopenmp -- 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 INSTALL_PREFIX -- Build files have been written to: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 make[1]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' # convert a few ISO-8859-1 files to address national-encoding set -e \ ; for file in res/TemplateBatchFiles/PARRIS.bf res/TemplateBatchFiles/TemplateModels/MEC.mdl res/TemplateBatchFiles/TemplateModels/models.lst \ ; do iconv -f ISO-8859-1 -t UTF-8 < ${file} > "${file}.new" \ ; mv "${file}.new" "${file}" \ ; done dh_auto_build -- MP MPI cd obj-x86_64-linux-gnu && make -j10 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 make[2]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-fyzopI/hyphy-2.5.36+dfsg -B/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f 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/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/associative_list.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/_hyExecutionContext.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/avllist.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/avllistx.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/avllistxl.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include 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-D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/ntuplestorage.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/operation.cpp.o -MF CMakeFiles/hyphy.dir/src/core/operation.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser.cpp.o -MF 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/topology.cpp.o -MF CMakeFiles/hyphy.dir/src/core/topology.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include 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CMakeFiles/hyphy.dir/src/new/scfg.cpp.o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -o hyphy -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 -lz -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu 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'/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/avllistx_iterator.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/avllistxl_iterator.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/fisher_exact.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/formula.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/formula_parsing_context.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o /usr/bin/c++ 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40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ 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/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -MF 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-Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib/mersenne_twister.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS 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CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/fisher_exact.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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-ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -MF CMakeFiles/hyphy.dir/src/core/nexus.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/ntuplestorage.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/operation.cpp.o -MF CMakeFiles/hyphy.dir/src/core/operation.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" 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-ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/strings.cpp.o -MF CMakeFiles/hyphy.dir/src/core/strings.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/strings.cpp [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -MF CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/time_difference.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/topology.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/topology.cpp.o -MF CMakeFiles/hyphy.dir/src/core/topology.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -MF CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/translation_table.cpp [ 70%] 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/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/variablecontainer.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/vector.cpp.o -MF CMakeFiles/hyphy.dir/src/core/vector.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS 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/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o.d -o 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-lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx' cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx/CMakeFiles/MP.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx' 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/alignment.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/baseobj.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/batchlan.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS 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-ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/category.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/strings.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/time_difference.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/variablecontainer.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bayesgraph.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bgm.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF 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CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -o HYPHYMPI -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib: -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 -lz /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lgomp -lpthread make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx' cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-avx/CMakeFiles/MPI.dir/DependInfo.cmake --color= make[5]: 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/category.cpp.o -MF CMakeFiles/hyphy.dir/src/core/category.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/category.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -MF CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -MF CMakeFiles/hyphy.dir/src/core/nexus.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ 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CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/operation.cpp.o -MF CMakeFiles/hyphy.dir/src/core/operation.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c 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CMakeFiles/hyphy.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/variablecontainer.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/vector.cpp.o -MF CMakeFiles/hyphy.dir/src/core/vector.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bayesgraph.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bayesgraph2.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -MF CMakeFiles/hyphy.dir/src/new/scfg.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib/mersenne_twister.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -o hyphy -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 -lz -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3/CMakeFiles/MP.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' [100%] Built target MP make[4]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' /usr/bin/cmake -E cmake_progress_start /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' /usr/bin/cmake -S/build/hyphy-fyzopI/hyphy-2.5.36+dfsg -B/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3 /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-sse3' [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/associative_list.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g 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CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/batchlanhelpers.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" 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CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c 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-D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/ntuplestorage.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/strings.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g 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-I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -MF 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib/mersenne_twister.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include 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-I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/core/include -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/contrib -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/lib/Link -I/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/src/mains/unix.cpp [100%] Linking CXX executable HYPHYMPI /usr/bin/cmake -E cmake_link_script CMakeFiles/HYPHYMPI.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hyphy-fyzopI/hyphy-2.5.36+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/partitionSequences.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/posteriors.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper3.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper4.ibf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/queryTree.bf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/readIndexFile.bf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relratioBootstrap.bf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/selectModelParameters.bf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/data -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/data/brown.nuc -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/data/integrase_BDA.nex -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/data/p51.aa -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/share/hyphy/data/p51.nex -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/bin/hyphy -- Installing: /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/bin/HYPHYMPI -- Set runtime path of "/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/tmp/usr/bin/HYPHYMPI" to "" make[1]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' dh_install -a chrpath --delete obj-*/HYPHYMPI mkdir -p debian/hyphy-mpi/usr/lib/hyphy/bin mkdir -p debian/hyphy-pt/usr/lib/hyphy/bin cp obj-avx/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/HYPHYMPI-avx cp obj-sse3/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/HYPHYMPI-sse3 cp obj-avx/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/hyphy-avx cp obj-sse3/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/hyphy-sse3 mv debian/hyphy-mpi/usr/bin/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/ mv debian/hyphy-pt/usr/bin/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/ cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/hyphy-mpi/usr/bin && \ ln -s ../lib/hyphy/bin/simd-dispatch HYPHYMPI cd /build/hyphy-fyzopI/hyphy-2.5.36+dfsg/debian/hyphy-pt/usr/bin && \ ln -s ../lib/hyphy/bin/simd-dispatch hyphy make[1]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' debian/rules override_dh_installdocs-arch make[1]: Entering directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' dh_installdocs -a for news in debian/NEWS.Debian.* ; do \ pkg=`echo ${news} | sed 's/.*NEWS.Debian.//'` ; \ cp -a ${news} debian/${pkg}/usr/share/doc/${pkg}/NEWS.Debian ; \ done make[1]: Leaving directory '/build/hyphy-fyzopI/hyphy-2.5.36+dfsg' dh_installchangelogs -a -O--buildsystem=cmake dh_installexamples -a -O--buildsystem=cmake dh_installman -a -O--buildsystem=cmake dh_installsystemduser -a -O--buildsystem=cmake dh_lintian -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake dpkg-deb: building package 'hyphy-pt' in '../hyphy-pt_2.5.36+dfsg-1_amd64.deb'. dpkg-deb: building package 'hyphy-pt-dbgsym' in '../hyphy-pt-dbgsym_2.5.36+dfsg-1_amd64.deb'. dpkg-deb: building package 'hyphy-mpi-dbgsym' in '../hyphy-mpi-dbgsym_2.5.36+dfsg-1_amd64.deb'. dpkg-deb: building package 'hyphy-mpi' in '../hyphy-mpi_2.5.36+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../hyphy_2.5.36+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../hyphy_2.5.36+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/hyphy-fyzopI /tmp/hyphy-2.5.36+dfsg-1pwyew7dt I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.fKOCaaQ8Ql... I: success in 910.7236 seconds md5: hyphy-mpi-dbgsym_2.5.36+dfsg-1_amd64.deb: OK md5: hyphy-mpi_2.5.36+dfsg-1_amd64.deb: OK md5: hyphy-pt-dbgsym_2.5.36+dfsg-1_amd64.deb: OK md5: hyphy-pt_2.5.36+dfsg-1_amd64.deb: OK sha1: hyphy-mpi-dbgsym_2.5.36+dfsg-1_amd64.deb: OK sha1: hyphy-mpi_2.5.36+dfsg-1_amd64.deb: OK sha1: hyphy-pt-dbgsym_2.5.36+dfsg-1_amd64.deb: OK sha1: hyphy-pt_2.5.36+dfsg-1_amd64.deb: OK sha256: hyphy-mpi-dbgsym_2.5.36+dfsg-1_amd64.deb: OK sha256: hyphy-mpi_2.5.36+dfsg-1_amd64.deb: OK sha256: hyphy-pt-dbgsym_2.5.36+dfsg-1_amd64.deb: OK sha256: hyphy-pt_2.5.36+dfsg-1_amd64.deb: OK Checksums: OK