Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/h/hyphy/hyphy_2.5.28+dfsg-3_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/hyphy-2.5.28+dfsg-3tdnzrik7/hyphy_2.5.28+dfsg-3_all.buildinfo Get source package info: hyphy=2.5.28+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/hyphy/2.5.28+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 chrpath=0.16-2+b1 cmake=3.18.4-2 cmake-data=3.18.4-2 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.75 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 gfortran-10=10.2.1-6 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 ibverbs-providers=33.1-1 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-7 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcbor0=0.5.0+dfsg-2 libcc1-0=10.2.1-6 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.18-1 libcrypt1=1:4.4.18-1 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libcurl3-gnutls=7.74.0-1.1 libcurl4=7.74.0-1.1 libcurl4-gnutls-dev=7.74.0-1.1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.256 libdebhelper-perl=13.3.4 libdpkg-perl=1.20.7.1 libedit2=3.1-20191231-2+b1 libelf1=0.183-3 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=2.2.10-2 libfabric1=1.11.0-2 libffi7=3.3-6 libfido2-1=1.6.0-2 libfile-stripnondeterminism-perl=1.11.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran-10-dev=10.2.1-6 libgfortran5=10.2.1-6 libglib2.0-0=2.66.7-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.1-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.7-2.1 libhwloc-dev=2.4.1+dfsg-1 libhwloc-plugins=2.4.1+dfsg-1 libhwloc15=2.4.1+dfsg-1 libibverbs-dev=33.1-1 libibverbs1=33.1-1 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui=1.12.1+dfsg-8 libjsoncpp24=1.9.4-4 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 libldap-2.4-2=2.4.57+dfsg-2 liblsan0=10.2.1-6 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-1 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7-2.1 libnghttp2-14=1.43.0-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.12-1+b1 libnuma1=2.0.12-1+b1 libopenmpi-dev=4.1.0-8 libopenmpi3=4.1.0-8 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-6 libpam-modules-bin=1.4.0-6 libpam-runtime=1.4.0-6 libpam0g=1.4.0-6 libpciaccess0=0.16-1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libpmix-dev=4.0.0-4 libpmix2=4.0.0-4 libprocps8=2:3.3.17-4 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libquadmath0=10.2.1-6 librdmacm1=33.1-1 librhash0=1.4.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsepol1=3.1-1 libsigsegv2=2.13-1 libsmartcols1=2.36.1-7 libsqlite3-0=3.34.1-3 libsqlite3-dev=3.34.1-3 libssh2-1=1.9.0-2 libssl-dev=1.1.1j-1 libssl1.1=1.1.1j-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-3 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libucx0=1.10.0~rc1-7 libudev1=247.3-3 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libuv1=1.40.0-1 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxml2=2.9.10+dfsg-6.3+b1 libxnvctrl0=460.56-1 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.19-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 mpi-default-dev=1.13 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 ocl-icd-libopencl1=2.2.14-2 openmpi-bin=4.1.0-8 openmpi-common=4.1.0-8 openssh-client=1:8.4p1-5 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-4 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-6 tar=1.34+dfsg-1 util-linux=2.36.1-7 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210315T203735Z/ 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=2.5.28+dfsg-3 && mkdir -p /build/hyphy-M5dP3H && dpkg-source --no-check -x /*.dsc /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg && chown -R builduser:builduser /build/hyphy-M5dP3H" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615927920" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/hyphy-M5dP3H /tmp/hyphy-2.5.28+dfsg-3tdnzrik7 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210315T203735Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.ty_ENowi7p 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.ty_ENowi7p Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210315T203735Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210315T203735Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (380 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 ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210315T203735Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.ty_ENowi7p Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210315T203735Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 30s (757 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.ty_ENowi7p I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d hyphy=2.5.28+dfsg-3 && mkdir -p /build/hyphy-M5dP3H && dpkg-source --no-check -x /*.dsc /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg && chown -R builduser:builduser /build/hyphy-M5dP3H"' exec /tmp/mmdebstrap.ty_ENowi7p 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 2478 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main hyphy 2.5.28+dfsg-3 (dsc) [2245 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main hyphy 2.5.28+dfsg-3 (tar) [2459 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main hyphy 2.5.28+dfsg-3 (diff) [17.3 kB] Fetched 2478 kB in 2s (1201 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'hyphy_2.5.28+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting hyphy in /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg dpkg-source: info: unpacking hyphy_2.5.28+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.5.28+dfsg-3.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 spelling I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1615927920" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.ty_ENowi7p dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.5.28+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . debian/rules clean dh clean --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' dh_auto_clean --builddirectory obj-avx dh_auto_clean --builddirectory obj-sse3 dh_auto_clean make[1]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary-indep dh binary-indep --buildsystem=cmake dh_update_autotools_config -i -O--buildsystem=cmake dh_autoreconf -i -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+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_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 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done 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 "7.74.0") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.34.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so Node not installed; API documentation will not be generated -- 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_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /build/hyphy-M5dP3H/hyphy-2.5.28+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_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 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_FMA3 -- Performing Test HAVE_FMA3 - Failed Set compiler flags to -fsigned-char -O3 -std=c++14 -mavx -- 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 "7.74.0") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.34.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so Node not installed; API documentation will not be generated -- 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 -pthread -fopenmp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_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-M5dP3H/hyphy-2.5.28+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_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 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success 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 "7.74.0") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.34.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so Node not installed; API documentation will not be generated -- 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_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 make[1]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+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 -j4 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 make[2]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/depend.internal". Scanning dependencies of target hyphy make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' [ 0%] 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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/_hyExecutionContext.cpp [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/alignment.cpp [ 0%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/associative_list.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx_iterator.cpp [ 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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/baseobj.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanhelpers.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/formula.cpp [ 30%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/formula_parsing_context.cpp [ 35%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o [ 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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/likefuncocl.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/likefunc2.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/trie.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/variable.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variablecontainer.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/mains/unix.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/mains/unix.cpp [100%] Linking CXX executable hyphy /usr/bin/cmake -E cmake_link_script CMakeFiles/hyphy.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -fsigned-char -O3 -std=c++14 -g CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o CMakeFiles/hyphy.dir/src/core/category.cpp.o CMakeFiles/hyphy.dir/src/core/constant.cpp.o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o CMakeFiles/hyphy.dir/src/core/formula.cpp.o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o CMakeFiles/hyphy.dir/src/core/list.cpp.o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o CMakeFiles/hyphy.dir/src/core/operation.cpp.o CMakeFiles/hyphy.dir/src/core/parser.cpp.o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o CMakeFiles/hyphy.dir/src/core/site.cpp.o CMakeFiles/hyphy.dir/src/core/stack.cpp.o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/hyphy.dir/src/core/strings.cpp.o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o CMakeFiles/hyphy.dir/src/core/topology.cpp.o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o CMakeFiles/hyphy.dir/src/core/tree.cpp.o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/trie.cpp.o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/variable.cpp.o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o CMakeFiles/hyphy.dir/src/core/vector.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o 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 -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+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-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MP.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MP.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MP.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MP.dir/depend.internal". Scanning dependencies of target MP make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' [100%] Built target MP make[4]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/HYPHYMPI.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/HYPHYMPI.dir/depend.internal". Scanning dependencies of target HYPHYMPI make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+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/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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/_hyExecutionContext.cpp [ 0%] 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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/associative_list.cpp [ 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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx_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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx_iterator.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.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__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/baseobj.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/calcnode.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/category.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variable.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bayesgraph.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_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bayesgraph2.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/mains/unix.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -fsigned-char -O3 -std=c++14 -pthread -g CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o 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 /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-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MPI.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MPI.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MPI.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MPI.dir/depend.internal". Scanning dependencies of target MPI make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/MPI.dir/build'. make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' [100%] Built target MPI make[4]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' dh_auto_build --builddirectory obj-avx -- MP MPI cd obj-avx && make -j4 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 make[2]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/hyphy.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/hyphy.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/hyphy.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/hyphy.dir/depend.internal". Scanning dependencies of target hyphy make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/associative_list.cpp [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/_hyExecutionContext.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx_iterator.cpp [ 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_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/baseobj.cpp [ 15%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanhelpers.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/formula.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/formula_parsing_context.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/trie.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/variable.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/hyphy.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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 -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/mains/unix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/mains/unix.cpp [100%] Linking CXX executable hyphy /usr/bin/cmake -E cmake_link_script CMakeFiles/hyphy.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -fsigned-char -O3 -std=c++14 -mavx -g CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o CMakeFiles/hyphy.dir/src/core/category.cpp.o CMakeFiles/hyphy.dir/src/core/constant.cpp.o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o CMakeFiles/hyphy.dir/src/core/formula.cpp.o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o CMakeFiles/hyphy.dir/src/core/list.cpp.o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o CMakeFiles/hyphy.dir/src/core/operation.cpp.o CMakeFiles/hyphy.dir/src/core/parser.cpp.o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o CMakeFiles/hyphy.dir/src/core/site.cpp.o CMakeFiles/hyphy.dir/src/core/stack.cpp.o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/hyphy.dir/src/core/strings.cpp.o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o CMakeFiles/hyphy.dir/src/core/topology.cpp.o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o CMakeFiles/hyphy.dir/src/core/tree.cpp.o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/trie.cpp.o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/variable.cpp.o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o CMakeFiles/hyphy.dir/src/core/vector.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o 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 -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MP.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MP.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MP.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MP.dir/depend.internal". Scanning dependencies of target MP make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' [100%] Built target MP make[4]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/HYPHYMPI.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/HYPHYMPI.dir/depend.internal". Scanning dependencies of target HYPHYMPI make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o [ 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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/_hyExecutionContext.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/associative_list.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx_iterator.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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 -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bayesgraph.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_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bayesgraph2.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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -fsigned-char -O3 -std=c++14 -mavx -pthread -g CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o 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 /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-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MPI.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MPI.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MPI.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles/MPI.dir/depend.internal". Scanning dependencies of target MPI make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make[5]: Nothing to be done for 'CMakeFiles/MPI.dir/build'. make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' [100%] Built target MPI make[4]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' make[2]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-avx' dh_auto_build --builddirectory obj-sse3 -- MP MPI cd obj-sse3 && make -j4 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 make[2]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/hyphy.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/hyphy.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/hyphy.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/hyphy.dir/depend.internal". Scanning dependencies of target hyphy make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' [ 0%] 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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/_hyExecutionContext.cpp [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllist.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/alignment.cpp [ 5%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/associative_list.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx_iterator.cpp [ 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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/baseobj.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanhelpers.cpp [ 20%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/formula.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/formula_parsing_context.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object 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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/trie.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/variable.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/hyphy.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__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/mains/unix.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/mains/unix.cpp [100%] Linking CXX executable hyphy /usr/bin/cmake -E cmake_link_script CMakeFiles/hyphy.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -fsigned-char -O3 -std=c++14 -msse3 -g CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o CMakeFiles/hyphy.dir/src/core/category.cpp.o CMakeFiles/hyphy.dir/src/core/constant.cpp.o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o CMakeFiles/hyphy.dir/src/core/formula.cpp.o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o CMakeFiles/hyphy.dir/src/core/list.cpp.o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o CMakeFiles/hyphy.dir/src/core/operation.cpp.o CMakeFiles/hyphy.dir/src/core/parser.cpp.o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o CMakeFiles/hyphy.dir/src/core/site.cpp.o CMakeFiles/hyphy.dir/src/core/stack.cpp.o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/hyphy.dir/src/core/strings.cpp.o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o CMakeFiles/hyphy.dir/src/core/topology.cpp.o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o CMakeFiles/hyphy.dir/src/core/tree.cpp.o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/trie.cpp.o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/variable.cpp.o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o CMakeFiles/hyphy.dir/src/core/vector.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o 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 -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MP.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MP.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MP.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MP.dir/depend.internal". Scanning dependencies of target MP make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' [100%] Built target MP make[4]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/HYPHYMPI.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/HYPHYMPI.dir/depend.internal". Scanning dependencies of target HYPHYMPI make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' [ 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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/associative_list.cpp [ 0%] 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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/alignment.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/_hyExecutionContext.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx_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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistx_iterator.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl.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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/baseobj.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/calcnode.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/category.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variable.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bayesgraph.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_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bayesgraph2.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_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o [ 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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/scfg.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/bgm2.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/mains/unix.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__ -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -ffile-prefix-map=/build/hyphy-M5dP3H/hyphy-2.5.28+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 -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/hyphy-M5dP3H/hyphy-2.5.28+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-M5dP3H/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -fsigned-char -O3 -std=c++14 -msse3 -pthread -g CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o 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 /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-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' cd /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MPI.dir/DependInfo.cmake --color= Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MPI.dir/DependInfo.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MPI.dir/depend.internal". Dependee "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MPI.dir/depend.internal". Scanning dependencies of target MPI make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/build make[5]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make[5]: Nothing to be done for 'CMakeFiles/MPI.dir/build'. make[5]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' [100%] Built target MPI make[4]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' /usr/bin/cmake -E cmake_progress_start /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make[2]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-sse3' make[1]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' set -e ; for SIMD in avx sse3 ; do \ if lscpu | grep -q ${SIMD} ; then \ find "obj-${SIMD}/" \ -not -path "*/CMakeFiles/*" \ -type f,l \ -executable \ -exec cp -v '{}' . \; && \ ./run_unit_tests.sh ; \ fi ; \ done 'obj-avx/HYPHYMPI' -> './HYPHYMPI' 'obj-avx/HYPHYMP' -> './HYPHYMP' 'obj-avx/hyphy' -> './hyphy' ./tests/hbltests/UnitTests/HBLCommands/Abs.bf ./tests/hbltests/UnitTests/HBLCommands/Add.bf ./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf ./tests/hbltests/UnitTests/HBLCommands/Arctan.bf ./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf ./tests/hbltests/UnitTests/HBLCommands/Beta.bf ./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf ./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf ./tests/hbltests/UnitTests/HBLCommands/Branchname.bf ./tests/hbltests/UnitTests/HBLCommands/CChi2.bf ./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/Call.bf ./tests/hbltests/UnitTests/HBLCommands/Caret.bf ./tests/hbltests/UnitTests/HBLCommands/Category.bf ./tests/hbltests/UnitTests/HBLCommands/Columns.bf ./tests/hbltests/UnitTests/HBLCommands/Continue.bf ./tests/hbltests/UnitTests/HBLCommands/Cos.bf ./tests/hbltests/UnitTests/HBLCommands/DataSet.bf ./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf ./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf ./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf ./tests/hbltests/UnitTests/HBLCommands/Divide.bf ./tests/hbltests/UnitTests/HBLCommands/Do.bf ./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf ./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf ./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf ./tests/hbltests/UnitTests/HBLCommands/Erf.bf ./tests/hbltests/UnitTests/HBLCommands/Eval.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf ./tests/hbltests/UnitTests/HBLCommands/Exp.bf ./tests/hbltests/UnitTests/HBLCommands/Export.bf ./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf ./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf ./tests/hbltests/UnitTests/HBLCommands/For.bf ./tests/hbltests/UnitTests/HBLCommands/Format.bf ./tests/hbltests/UnitTests/HBLCommands/Function.bf ./tests/hbltests/UnitTests/HBLCommands/Gamma.bf ./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf ./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf ./tests/hbltests/UnitTests/HBLCommands/GetString.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf ./tests/hbltests/UnitTests/HBLCommands/IBeta.bf ./tests/hbltests/UnitTests/HBLCommands/IGamma.bf ./tests/hbltests/UnitTests/HBLCommands/If.bf ./tests/hbltests/UnitTests/HBLCommands/Integrate.bf ./tests/hbltests/UnitTests/HBLCommands/Inverse.bf ./tests/hbltests/UnitTests/HBLCommands/JSON.bf ./tests/hbltests/UnitTests/HBLCommands/Join.bf ./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf ./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf ./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf ./tests/hbltests/UnitTests/HBLCommands/Log.bf ./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf ./tests/hbltests/UnitTests/HBLCommands/Max.bf ./tests/hbltests/UnitTests/HBLCommands/Min.bf ./tests/hbltests/UnitTests/HBLCommands/Model.bf ./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf ./tests/hbltests/UnitTests/HBLCommands/Random.bf ./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf ./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf ./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf ./tests/hbltests/UnitTests/HBLCommands/Return.bf ./tests/hbltests/UnitTests/HBLCommands/Rows.bf ./tests/hbltests/UnitTests/HBLCommands/Simplex.bf ./tests/hbltests/UnitTests/HBLCommands/Simplify.bf ./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf ./tests/hbltests/UnitTests/HBLCommands/Sin.bf ./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf ./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf ./tests/hbltests/UnitTests/HBLCommands/Subtract.bf ./tests/hbltests/UnitTests/HBLCommands/Tan.bf ./tests/hbltests/UnitTests/HBLCommands/Time.bf ./tests/hbltests/UnitTests/HBLCommands/TipCount.bf ./tests/hbltests/UnitTests/HBLCommands/TipName.bf ./tests/hbltests/UnitTests/HBLCommands/Topology.bf ./tests/hbltests/UnitTests/HBLCommands/Transpose.bf ./tests/hbltests/UnitTests/HBLCommands/Tree.bf ./tests/hbltests/UnitTests/HBLCommands/Type.bf ./tests/hbltests/UnitTests/HBLCommands/While.bf ./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf ./tests/hbltests/UnitTests/HBLCommands/assert.bf ./tests/hbltests/UnitTests/HBLCommands/break.bf ./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf ./tests/hbltests/UnitTests/HBLCommands/include.bf ./tests/hbltests/UnitTests/HBLCommands/lfunction.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf ./tests/hbltests/UnitTests/HBLCommands/namespace.bf \n\n------------------------ALL TEST PASSED------------------------------------\n 'obj-sse3/HYPHYMPI' -> './HYPHYMPI' 'obj-sse3/HYPHYMP' -> './HYPHYMP' 'obj-sse3/hyphy' -> './hyphy' ./tests/hbltests/UnitTests/HBLCommands/Abs.bf ./tests/hbltests/UnitTests/HBLCommands/Add.bf ./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf ./tests/hbltests/UnitTests/HBLCommands/Arctan.bf ./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf ./tests/hbltests/UnitTests/HBLCommands/Beta.bf ./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf ./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf ./tests/hbltests/UnitTests/HBLCommands/Branchname.bf ./tests/hbltests/UnitTests/HBLCommands/CChi2.bf ./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/Call.bf ./tests/hbltests/UnitTests/HBLCommands/Caret.bf ./tests/hbltests/UnitTests/HBLCommands/Category.bf ./tests/hbltests/UnitTests/HBLCommands/Columns.bf ./tests/hbltests/UnitTests/HBLCommands/Continue.bf ./tests/hbltests/UnitTests/HBLCommands/Cos.bf ./tests/hbltests/UnitTests/HBLCommands/DataSet.bf ./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf ./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf ./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf ./tests/hbltests/UnitTests/HBLCommands/Divide.bf ./tests/hbltests/UnitTests/HBLCommands/Do.bf ./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf ./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf ./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf ./tests/hbltests/UnitTests/HBLCommands/Erf.bf ./tests/hbltests/UnitTests/HBLCommands/Eval.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf ./tests/hbltests/UnitTests/HBLCommands/Exp.bf ./tests/hbltests/UnitTests/HBLCommands/Export.bf ./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf ./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf ./tests/hbltests/UnitTests/HBLCommands/For.bf ./tests/hbltests/UnitTests/HBLCommands/Format.bf ./tests/hbltests/UnitTests/HBLCommands/Function.bf ./tests/hbltests/UnitTests/HBLCommands/Gamma.bf ./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf ./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf ./tests/hbltests/UnitTests/HBLCommands/GetString.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf ./tests/hbltests/UnitTests/HBLCommands/IBeta.bf ./tests/hbltests/UnitTests/HBLCommands/IGamma.bf ./tests/hbltests/UnitTests/HBLCommands/If.bf ./tests/hbltests/UnitTests/HBLCommands/Integrate.bf ./tests/hbltests/UnitTests/HBLCommands/Inverse.bf ./tests/hbltests/UnitTests/HBLCommands/JSON.bf ./tests/hbltests/UnitTests/HBLCommands/Join.bf ./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf ./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf ./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf ./tests/hbltests/UnitTests/HBLCommands/Log.bf ./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf ./tests/hbltests/UnitTests/HBLCommands/Max.bf ./tests/hbltests/UnitTests/HBLCommands/Min.bf ./tests/hbltests/UnitTests/HBLCommands/Model.bf ./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf ./tests/hbltests/UnitTests/HBLCommands/Random.bf ./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf ./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf ./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf ./tests/hbltests/UnitTests/HBLCommands/Return.bf ./tests/hbltests/UnitTests/HBLCommands/Rows.bf ./tests/hbltests/UnitTests/HBLCommands/Simplex.bf ./tests/hbltests/UnitTests/HBLCommands/Simplify.bf ./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf ./tests/hbltests/UnitTests/HBLCommands/Sin.bf ./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf ./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf ./tests/hbltests/UnitTests/HBLCommands/Subtract.bf ./tests/hbltests/UnitTests/HBLCommands/Tan.bf ./tests/hbltests/UnitTests/HBLCommands/Time.bf ./tests/hbltests/UnitTests/HBLCommands/TipCount.bf ./tests/hbltests/UnitTests/HBLCommands/TipName.bf ./tests/hbltests/UnitTests/HBLCommands/Topology.bf ./tests/hbltests/UnitTests/HBLCommands/Transpose.bf ./tests/hbltests/UnitTests/HBLCommands/Tree.bf ./tests/hbltests/UnitTests/HBLCommands/Type.bf ./tests/hbltests/UnitTests/HBLCommands/While.bf ./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf ./tests/hbltests/UnitTests/HBLCommands/assert.bf ./tests/hbltests/UnitTests/HBLCommands/break.bf ./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf ./tests/hbltests/UnitTests/HBLCommands/include.bf ./tests/hbltests/UnitTests/HBLCommands/lfunction.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf ./tests/hbltests/UnitTests/HBLCommands/namespace.bf \n\n------------------------ALL TEST PASSED------------------------------------\n find "obj-x86_64-linux-gnu/" \ -not -path "*/CMakeFiles/*" \ -type f,l \ -executable \ -exec cp -v '{}' . \; 'obj-x86_64-linux-gnu/HYPHYMPI' -> './HYPHYMPI' 'obj-x86_64-linux-gnu/HYPHYMP' -> './HYPHYMP' 'obj-x86_64-linux-gnu/hyphy' -> './hyphy' ./run_unit_tests.sh ./tests/hbltests/UnitTests/HBLCommands/Abs.bf ./tests/hbltests/UnitTests/HBLCommands/Add.bf ./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf ./tests/hbltests/UnitTests/HBLCommands/Arctan.bf ./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf ./tests/hbltests/UnitTests/HBLCommands/Beta.bf ./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf ./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf ./tests/hbltests/UnitTests/HBLCommands/Branchname.bf ./tests/hbltests/UnitTests/HBLCommands/CChi2.bf ./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/Call.bf ./tests/hbltests/UnitTests/HBLCommands/Caret.bf ./tests/hbltests/UnitTests/HBLCommands/Category.bf ./tests/hbltests/UnitTests/HBLCommands/Columns.bf ./tests/hbltests/UnitTests/HBLCommands/Continue.bf ./tests/hbltests/UnitTests/HBLCommands/Cos.bf ./tests/hbltests/UnitTests/HBLCommands/DataSet.bf ./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf ./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf ./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf ./tests/hbltests/UnitTests/HBLCommands/Divide.bf ./tests/hbltests/UnitTests/HBLCommands/Do.bf ./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf ./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf ./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf ./tests/hbltests/UnitTests/HBLCommands/Erf.bf ./tests/hbltests/UnitTests/HBLCommands/Eval.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf ./tests/hbltests/UnitTests/HBLCommands/Exp.bf ./tests/hbltests/UnitTests/HBLCommands/Export.bf ./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf ./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf ./tests/hbltests/UnitTests/HBLCommands/For.bf ./tests/hbltests/UnitTests/HBLCommands/Format.bf ./tests/hbltests/UnitTests/HBLCommands/Function.bf ./tests/hbltests/UnitTests/HBLCommands/Gamma.bf ./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf ./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf ./tests/hbltests/UnitTests/HBLCommands/GetString.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf ./tests/hbltests/UnitTests/HBLCommands/IBeta.bf ./tests/hbltests/UnitTests/HBLCommands/IGamma.bf ./tests/hbltests/UnitTests/HBLCommands/If.bf ./tests/hbltests/UnitTests/HBLCommands/Integrate.bf ./tests/hbltests/UnitTests/HBLCommands/Inverse.bf ./tests/hbltests/UnitTests/HBLCommands/JSON.bf ./tests/hbltests/UnitTests/HBLCommands/Join.bf ./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf ./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf ./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf ./tests/hbltests/UnitTests/HBLCommands/Log.bf ./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf ./tests/hbltests/UnitTests/HBLCommands/Max.bf ./tests/hbltests/UnitTests/HBLCommands/Min.bf ./tests/hbltests/UnitTests/HBLCommands/Model.bf ./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf ./tests/hbltests/UnitTests/HBLCommands/Random.bf ./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf ./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf ./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf ./tests/hbltests/UnitTests/HBLCommands/Return.bf ./tests/hbltests/UnitTests/HBLCommands/Rows.bf ./tests/hbltests/UnitTests/HBLCommands/Simplex.bf ./tests/hbltests/UnitTests/HBLCommands/Simplify.bf ./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf ./tests/hbltests/UnitTests/HBLCommands/Sin.bf ./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf ./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf ./tests/hbltests/UnitTests/HBLCommands/Subtract.bf ./tests/hbltests/UnitTests/HBLCommands/Tan.bf ./tests/hbltests/UnitTests/HBLCommands/Time.bf ./tests/hbltests/UnitTests/HBLCommands/TipCount.bf ./tests/hbltests/UnitTests/HBLCommands/TipName.bf ./tests/hbltests/UnitTests/HBLCommands/Topology.bf ./tests/hbltests/UnitTests/HBLCommands/Transpose.bf ./tests/hbltests/UnitTests/HBLCommands/Tree.bf ./tests/hbltests/UnitTests/HBLCommands/Type.bf ./tests/hbltests/UnitTests/HBLCommands/While.bf ./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf ./tests/hbltests/UnitTests/HBLCommands/assert.bf ./tests/hbltests/UnitTests/HBLCommands/break.bf ./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf ./tests/hbltests/UnitTests/HBLCommands/include.bf ./tests/hbltests/UnitTests/HBLCommands/lfunction.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf ./tests/hbltests/UnitTests/HBLCommands/namespace.bf \n\n------------------------ALL TEST PASSED------------------------------------\n make[1]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=cmake dh_prep -i -O--buildsystem=cmake dh_auto_install -i -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/hyphy-M5dP3H/hyphy-2.5.28\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg -B/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGEmulator.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/doNNISwap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/F_ST.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GARD.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SimilarityPlot.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/DistanceMatrix.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/categoryEcho.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PartitionDataFile.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BGM.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/selectModelParameters.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/globalChecker.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_CMS_Aux.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestCladeMeans.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LRTRecombTest.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/RelativeRatio.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/UpperBound.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Gateaux.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/T3P -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/JC69 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93_RV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_codon -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN84 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_MH -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_aa -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_RV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_binary -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P_RV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SM-2019.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CleanStopCodons.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ClusterAnalysis.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LHT.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/RelativeRate.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SandNSAmbigs.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestClade.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionLRT.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MolecularClock.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGEmulator_MF.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonToProtein.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LZ_Complexity.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteREL.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MolClockAllRoots.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/NeighborJoining.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/doSPRSwap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GA_CHC.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/readIndexFile.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/KHTest.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/last.date -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/PostScript.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/NJ.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/GrabBag.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/CodonTools.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DBTools.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/MPITools.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SequentialAddition.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TreeTools.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper4.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ConvertDataFile.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TopologySearch.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/bayesgraph.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/files.lst -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/FitnessAAModels.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.dat -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Default -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/PCH -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/S4 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAF81 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16A -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/190 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AddABias.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/chooseDistanceFormula.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/srs.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/sir.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGASimProcessor.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/WANC.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SimmondsAI.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSequences.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LEISR.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestBranchDNDS.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/NucModelCompare.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonModelCompare.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/binomial.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSites.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relratioBootstrap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper3.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/NielsenYang.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/partitionSequences.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignShared.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GUI -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GUI/crayolaColors.def -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/stats.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/function-loader.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/distances.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/random.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/math.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/parameters.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MSS.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary/empirical.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR-MutSel.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/all-terms.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SequentialAddition.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_BMS_Aux.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/posteriors.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LocalMolClock.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GateauxMR.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/queryTree.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MGvsGY.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_MFReader_.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AAModelComparison.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CleanGaps.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/molclockBootstrap.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_tipDater.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGIvL.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ModelTest.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Vertebratemtdna.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Euplotid_Nuclear.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Mold_mtDNA.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Yeast_mtDNA.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ciliate.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ascidian_mtDNA.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Flatworm_mtDNA.cod -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69 -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary/F81.mdl -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/p51.nex -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/p51.aa -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/brown.nuc -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/integrase_BDA.nex -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Equal -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Equal -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/nuc.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/codon.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/dinuc.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Equal -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params. -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/aa.bf -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/bin/hyphy -- Installing: /build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/bin/HYPHYMPI -- Set runtime path of "/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/debian/tmp/usr/bin/HYPHYMPI" to "" make[1]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install-indep make[1]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' dh_install -i dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/hyphy/bin make[1]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' dh_installdocs -i make[1]: Leaving directory '/build/hyphy-M5dP3H/hyphy-2.5.28+dfsg' dh_installchangelogs -i -O--buildsystem=cmake dh_installexamples -i -O--buildsystem=cmake dh_installman -i -O--buildsystem=cmake dh_installsystemduser -i -O--buildsystem=cmake dh_lintian -i -O--buildsystem=cmake dh_perl -i -O--buildsystem=cmake dh_link -i -O--buildsystem=cmake dh_strip_nondeterminism -i -O--buildsystem=cmake dh_compress -i -O--buildsystem=cmake dh_fixperms -i -O--buildsystem=cmake dh_missing -i -O--buildsystem=cmake dh_installdeb -i -O--buildsystem=cmake dh_gencontrol -i -O--buildsystem=cmake dh_md5sums -i -O--buildsystem=cmake dh_builddeb -i -O--buildsystem=cmake dpkg-deb: building package 'hyphy-common' in '../hyphy-common_2.5.28+dfsg-3_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../hyphy_2.5.28+dfsg-3_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/hyphy-M5dP3H /tmp/hyphy-2.5.28+dfsg-3tdnzrik7 I: cleaning package lists and apt cache... W: deleting files in /tmp: HYPHY-mkk7dC W: deleting files in /tmp: HYPHY-WywtRR W: deleting files in /tmp: HYPHY-wiSppC W: deleting files in /tmp: HYPHY-reaIqY W: deleting files in /tmp: HYPHY-buoebT W: deleting files in /tmp: HYPHY-mnj4kS W: deleting files in /tmp: HYPHY-8z6EFQ W: deleting files in /tmp: HYPHY-EcTceS W: deleting files in /tmp: HYPHY-DTOXtW I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.ty_ENowi7p... I: success in 3342.3963 seconds md5: hyphy-common_2.5.28+dfsg-3_all.deb: OK sha1: hyphy-common_2.5.28+dfsg-3_all.deb: OK sha256: hyphy-common_2.5.28+dfsg-3_all.deb: OK Checksums: OK