Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/h/hyphy/hyphy_2.5.40+dfsg-1_all.buildinfo Use metasnap for getting required timestamps Cannot get timestamps from metasnap: 404 (Not Found) Use snapshot for getting required timestamps Get source package info: hyphy=2.5.40+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/hyphy/2.5.40+dfsg-1/srcfiles?fileinfo=1 Initialize APT cache Get binary package info: adduser=3.122 Binary URL: http://snapshot.notset.fr/mr/binary/adduser/3.122/binfiles?fileinfo=1 Get binary package info: autoconf=2.71-2 Binary URL: http://snapshot.notset.fr/mr/binary/autoconf/2.71-2/binfiles?fileinfo=1 Get binary package info: automake=1:1.16.5-1.3 Binary URL: http://snapshot.notset.fr/mr/binary/automake/1:1.16.5-1.3/binfiles?fileinfo=1 Get binary package info: autopoint=0.21-6 Binary URL: http://snapshot.notset.fr/mr/binary/autopoint/0.21-6/binfiles?fileinfo=1 Get binary package info: autotools-dev=20220109.1 Binary URL: http://snapshot.notset.fr/mr/binary/autotools-dev/20220109.1/binfiles?fileinfo=1 Get binary package info: base-files=12.2 Binary URL: http://snapshot.notset.fr/mr/binary/base-files/12.2/binfiles?fileinfo=1 Get binary package info: base-passwd=3.5.52 Binary URL: http://snapshot.notset.fr/mr/binary/base-passwd/3.5.52/binfiles?fileinfo=1 Get binary package info: bash=5.1-6.1 Binary URL: http://snapshot.notset.fr/mr/binary/bash/5.1-6.1/binfiles?fileinfo=1 Get binary package info: binutils=2.38.50.20220707-1 Binary URL: http://snapshot.notset.fr/mr/binary/binutils/2.38.50.20220707-1/binfiles?fileinfo=1 Get binary package info: binutils-common=2.38.50.20220707-1 Binary URL: http://snapshot.notset.fr/mr/binary/binutils-common/2.38.50.20220707-1/binfiles?fileinfo=1 Get binary package info: binutils-x86-64-linux-gnu=2.38.50.20220707-1 Binary URL: http://snapshot.notset.fr/mr/binary/binutils-x86-64-linux-gnu/2.38.50.20220707-1/binfiles?fileinfo=1 Get binary package info: bsdextrautils=2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/bsdextrautils/2.38-4/binfiles?fileinfo=1 Get binary package info: bsdutils=1:2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/bsdutils/1:2.38-4/binfiles?fileinfo=1 Get binary package info: build-essential=12.9 Binary URL: http://snapshot.notset.fr/mr/binary/build-essential/12.9/binfiles?fileinfo=1 Get binary package info: bzip2=1.0.8-5 Binary URL: http://snapshot.notset.fr/mr/binary/bzip2/1.0.8-5/binfiles?fileinfo=1 Get binary package info: chrpath=0.16-2+b1 Binary URL: http://snapshot.notset.fr/mr/binary/chrpath/0.16-2+b1/binfiles?fileinfo=1 Get binary package info: cmake=3.23.2-1 Binary URL: http://snapshot.notset.fr/mr/binary/cmake/3.23.2-1/binfiles?fileinfo=1 Get binary package info: cmake-data=3.23.2-1 Binary URL: http://snapshot.notset.fr/mr/binary/cmake-data/3.23.2-1/binfiles?fileinfo=1 Get binary package info: coreutils=8.32-4.1 Binary URL: http://snapshot.notset.fr/mr/binary/coreutils/8.32-4.1/binfiles?fileinfo=1 Get binary package info: cpp=4:11.2.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/cpp/4:11.2.0-2/binfiles?fileinfo=1 Get binary package info: cpp-11=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/cpp-11/11.3.0-4/binfiles?fileinfo=1 Get binary package info: cpp-12=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/cpp-12/12.1.0-5/binfiles?fileinfo=1 Get binary package info: dash=0.5.11+git20210903+057cd650a4ed-8 Binary URL: http://snapshot.notset.fr/mr/binary/dash/0.5.11+git20210903+057cd650a4ed-8/binfiles?fileinfo=1 Get binary package info: debconf=1.5.79 Binary URL: http://snapshot.notset.fr/mr/binary/debconf/1.5.79/binfiles?fileinfo=1 Get binary package info: debhelper=13.8 Binary URL: http://snapshot.notset.fr/mr/binary/debhelper/13.8/binfiles?fileinfo=1 Get binary package info: debianutils=5.7-0.2 Binary URL: http://snapshot.notset.fr/mr/binary/debianutils/5.7-0.2/binfiles?fileinfo=1 Get binary package info: dh-autoreconf=20 Binary URL: http://snapshot.notset.fr/mr/binary/dh-autoreconf/20/binfiles?fileinfo=1 Get binary package info: dh-elpa-helper=2.0.10 Binary URL: http://snapshot.notset.fr/mr/binary/dh-elpa-helper/2.0.10/binfiles?fileinfo=1 Get binary package info: dh-strip-nondeterminism=1.13.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/dh-strip-nondeterminism/1.13.0-1/binfiles?fileinfo=1 Get binary package info: diffutils=1:3.7-5 Binary URL: http://snapshot.notset.fr/mr/binary/diffutils/1:3.7-5/binfiles?fileinfo=1 Get binary package info: dpkg=1.21.9 Binary URL: http://snapshot.notset.fr/mr/binary/dpkg/1.21.9/binfiles?fileinfo=1 Get binary package info: dpkg-dev=1.21.9 Binary URL: http://snapshot.notset.fr/mr/binary/dpkg-dev/1.21.9/binfiles?fileinfo=1 Get binary package info: dwz=0.14-1 Binary URL: http://snapshot.notset.fr/mr/binary/dwz/0.14-1/binfiles?fileinfo=1 Get binary package info: emacsen-common=3.0.4 Binary URL: http://snapshot.notset.fr/mr/binary/emacsen-common/3.0.4/binfiles?fileinfo=1 Get binary package info: file=1:5.41-4 Binary URL: http://snapshot.notset.fr/mr/binary/file/1:5.41-4/binfiles?fileinfo=1 Get binary package info: findutils=4.9.0-3 Binary URL: http://snapshot.notset.fr/mr/binary/findutils/4.9.0-3/binfiles?fileinfo=1 Get binary package info: g++=4:11.2.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/g++/4:11.2.0-2/binfiles?fileinfo=1 Get binary package info: g++-11=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/g++-11/11.3.0-4/binfiles?fileinfo=1 Get binary package info: gcc=4:11.2.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/gcc/4:11.2.0-2/binfiles?fileinfo=1 Get binary package info: gcc-11=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/gcc-11/11.3.0-4/binfiles?fileinfo=1 Get binary package info: gcc-11-base=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/gcc-11-base/11.3.0-4/binfiles?fileinfo=1 Get binary package info: gcc-12=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/gcc-12/12.1.0-5/binfiles?fileinfo=1 Get binary package info: gcc-12-base=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/gcc-12-base/12.1.0-5/binfiles?fileinfo=1 Get binary package info: gettext=0.21-6 Binary URL: http://snapshot.notset.fr/mr/binary/gettext/0.21-6/binfiles?fileinfo=1 Get binary package info: gettext-base=0.21-6 Binary URL: http://snapshot.notset.fr/mr/binary/gettext-base/0.21-6/binfiles?fileinfo=1 Get binary package info: gfortran-12=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/gfortran-12/12.1.0-5/binfiles?fileinfo=1 Get binary package info: grep=3.7-1 Binary URL: http://snapshot.notset.fr/mr/binary/grep/3.7-1/binfiles?fileinfo=1 Get binary package info: groff-base=1.22.4-8 Binary URL: http://snapshot.notset.fr/mr/binary/groff-base/1.22.4-8/binfiles?fileinfo=1 Get binary package info: gzip=1.12-1 Binary URL: http://snapshot.notset.fr/mr/binary/gzip/1.12-1/binfiles?fileinfo=1 Get binary package info: hostname=3.23 Binary URL: http://snapshot.notset.fr/mr/binary/hostname/3.23/binfiles?fileinfo=1 Get binary package info: ibverbs-providers=40.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/ibverbs-providers/40.0-1/binfiles?fileinfo=1 Get binary package info: init-system-helpers=1.64 Binary URL: http://snapshot.notset.fr/mr/binary/init-system-helpers/1.64/binfiles?fileinfo=1 Get binary package info: intltool-debian=0.35.0+20060710.5 Binary URL: http://snapshot.notset.fr/mr/binary/intltool-debian/0.35.0+20060710.5/binfiles?fileinfo=1 Get binary package info: libacl1=2.3.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libacl1/2.3.1-1/binfiles?fileinfo=1 Get binary package info: libarchive-zip-perl=1.68-1 Binary URL: http://snapshot.notset.fr/mr/binary/libarchive-zip-perl/1.68-1/binfiles?fileinfo=1 Get binary package info: libarchive13=3.6.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libarchive13/3.6.0-1/binfiles?fileinfo=1 Get binary package info: libasan6=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libasan6/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libasan8=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libasan8/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libatomic1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libatomic1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libattr1=1:2.5.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libattr1/1:2.5.1-1/binfiles?fileinfo=1 Get binary package info: libaudit-common=1:3.0.7-1 Binary URL: http://snapshot.notset.fr/mr/binary/libaudit-common/1:3.0.7-1/binfiles?fileinfo=1 Get binary package info: libaudit1=1:3.0.7-1+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libaudit1/1:3.0.7-1+b1/binfiles?fileinfo=1 Get binary package info: libbinutils=2.38.50.20220707-1 Binary URL: http://snapshot.notset.fr/mr/binary/libbinutils/2.38.50.20220707-1/binfiles?fileinfo=1 Get binary package info: libblkid1=2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/libblkid1/2.38-4/binfiles?fileinfo=1 Get binary package info: libbrotli1=1.0.9-2+b3 Binary URL: http://snapshot.notset.fr/mr/binary/libbrotli1/1.0.9-2+b3/binfiles?fileinfo=1 Get binary package info: libbsd0=0.11.6-1 Binary URL: http://snapshot.notset.fr/mr/binary/libbsd0/0.11.6-1/binfiles?fileinfo=1 Get binary package info: libbz2-1.0=1.0.8-5 Binary URL: http://snapshot.notset.fr/mr/binary/libbz2-1.0/1.0.8-5/binfiles?fileinfo=1 Get binary package info: libc-bin=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc-bin/2.33-8/binfiles?fileinfo=1 Get binary package info: libc-dev-bin=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc-dev-bin/2.33-8/binfiles?fileinfo=1 Get binary package info: libc6=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc6/2.33-8/binfiles?fileinfo=1 Get binary package info: libc6-dev=2.33-8 Binary URL: http://snapshot.notset.fr/mr/binary/libc6-dev/2.33-8/binfiles?fileinfo=1 Get binary package info: libcap-ng0=0.8.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libcap-ng0/0.8.3-1/binfiles?fileinfo=1 Get binary package info: libcap2=1:2.44-1 Binary URL: http://snapshot.notset.fr/mr/binary/libcap2/1:2.44-1/binfiles?fileinfo=1 Get binary package info: libcbor0.8=0.8.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcbor0.8/0.8.0-2/binfiles?fileinfo=1 Get binary package info: libcc1-0=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libcc1-0/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libcom-err2=1.46.5-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcom-err2/1.46.5-2/binfiles?fileinfo=1 Get binary package info: libcrypt-dev=1:4.4.28-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcrypt-dev/1:4.4.28-2/binfiles?fileinfo=1 Get binary package info: libcrypt1=1:4.4.28-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcrypt1/1:4.4.28-2/binfiles?fileinfo=1 Get binary package info: libctf-nobfd0=2.38.50.20220707-1 Binary URL: http://snapshot.notset.fr/mr/binary/libctf-nobfd0/2.38.50.20220707-1/binfiles?fileinfo=1 Get binary package info: libctf0=2.38.50.20220707-1 Binary URL: http://snapshot.notset.fr/mr/binary/libctf0/2.38.50.20220707-1/binfiles?fileinfo=1 Get binary package info: libcurl3-gnutls=7.84.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcurl3-gnutls/7.84.0-2/binfiles?fileinfo=1 Get binary package info: libcurl4=7.84.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcurl4/7.84.0-2/binfiles?fileinfo=1 Get binary package info: libcurl4-gnutls-dev=7.84.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libcurl4-gnutls-dev/7.84.0-2/binfiles?fileinfo=1 Get binary package info: libdb5.3=5.3.28+dfsg1-0.10 Binary URL: http://snapshot.notset.fr/mr/binary/libdb5.3/5.3.28+dfsg1-0.10/binfiles?fileinfo=1 Get binary package info: libdebconfclient0=0.263 Binary URL: http://snapshot.notset.fr/mr/binary/libdebconfclient0/0.263/binfiles?fileinfo=1 Get binary package info: libdebhelper-perl=13.8 Binary URL: http://snapshot.notset.fr/mr/binary/libdebhelper-perl/13.8/binfiles?fileinfo=1 Get binary package info: libdpkg-perl=1.21.9 Binary URL: http://snapshot.notset.fr/mr/binary/libdpkg-perl/1.21.9/binfiles?fileinfo=1 Get binary package info: libedit2=3.1-20210910-1 Binary URL: http://snapshot.notset.fr/mr/binary/libedit2/3.1-20210910-1/binfiles?fileinfo=1 Get binary package info: libelf1=0.187-1 Binary URL: http://snapshot.notset.fr/mr/binary/libelf1/0.187-1/binfiles?fileinfo=1 Get binary package info: libevent-2.1-7=2.1.12-stable-5+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libevent-2.1-7/2.1.12-stable-5+b1/binfiles?fileinfo=1 Get binary package info: libevent-core-2.1-7=2.1.12-stable-5+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libevent-core-2.1-7/2.1.12-stable-5+b1/binfiles?fileinfo=1 Get binary package info: libevent-dev=2.1.12-stable-5+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libevent-dev/2.1.12-stable-5+b1/binfiles?fileinfo=1 Get binary package info: libevent-extra-2.1-7=2.1.12-stable-5+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libevent-extra-2.1-7/2.1.12-stable-5+b1/binfiles?fileinfo=1 Get binary package info: libevent-openssl-2.1-7=2.1.12-stable-5+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libevent-openssl-2.1-7/2.1.12-stable-5+b1/binfiles?fileinfo=1 Get binary package info: libevent-pthreads-2.1-7=2.1.12-stable-5+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libevent-pthreads-2.1-7/2.1.12-stable-5+b1/binfiles?fileinfo=1 Get binary package info: libexpat1=2.4.8-1 Binary URL: http://snapshot.notset.fr/mr/binary/libexpat1/2.4.8-1/binfiles?fileinfo=1 Get binary package info: libfabric1=1.11.0-3 Binary URL: http://snapshot.notset.fr/mr/binary/libfabric1/1.11.0-3/binfiles?fileinfo=1 Get binary package info: libffi8=3.4.2-4 Binary URL: http://snapshot.notset.fr/mr/binary/libffi8/3.4.2-4/binfiles?fileinfo=1 Get binary package info: libfido2-1=1.11.0-1+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libfido2-1/1.11.0-1+b1/binfiles?fileinfo=1 Get binary package info: libfile-stripnondeterminism-perl=1.13.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libfile-stripnondeterminism-perl/1.13.0-1/binfiles?fileinfo=1 Get binary package info: libgcc-11-dev=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libgcc-11-dev/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libgcc-12-dev=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libgcc-12-dev/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libgcc-s1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libgcc-s1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libgcrypt20=1.10.1-2 Binary URL: http://snapshot.notset.fr/mr/binary/libgcrypt20/1.10.1-2/binfiles?fileinfo=1 Get binary package info: libgdbm-compat4=1.23-1 Binary URL: http://snapshot.notset.fr/mr/binary/libgdbm-compat4/1.23-1/binfiles?fileinfo=1 Get binary package info: libgdbm6=1.23-1 Binary URL: http://snapshot.notset.fr/mr/binary/libgdbm6/1.23-1/binfiles?fileinfo=1 Get binary package info: libgfortran-12-dev=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libgfortran-12-dev/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libgfortran5=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libgfortran5/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libglib2.0-0=2.72.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libglib2.0-0/2.72.3-1/binfiles?fileinfo=1 Get binary package info: libgmp10=2:6.2.1+dfsg1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libgmp10/2:6.2.1+dfsg1-1/binfiles?fileinfo=1 Get binary package info: libgnutls30=3.7.6-2 Binary URL: http://snapshot.notset.fr/mr/binary/libgnutls30/3.7.6-2/binfiles?fileinfo=1 Get binary package info: libgomp1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libgomp1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libgpg-error0=1.45-2 Binary URL: http://snapshot.notset.fr/mr/binary/libgpg-error0/1.45-2/binfiles?fileinfo=1 Get binary package info: libgprofng0=2.38.50.20220707-1 Binary URL: http://snapshot.notset.fr/mr/binary/libgprofng0/2.38.50.20220707-1/binfiles?fileinfo=1 Get binary package info: libgssapi-krb5-2=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libgssapi-krb5-2/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: libhogweed6=3.7.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libhogweed6/3.7.3-1/binfiles?fileinfo=1 Get binary package info: libhwloc-dev=2.8.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libhwloc-dev/2.8.0-1/binfiles?fileinfo=1 Get binary package info: libhwloc-plugins=2.8.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libhwloc-plugins/2.8.0-1/binfiles?fileinfo=1 Get binary package info: libhwloc15=2.8.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libhwloc15/2.8.0-1/binfiles?fileinfo=1 Get binary package info: libibverbs-dev=40.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libibverbs-dev/40.0-1/binfiles?fileinfo=1 Get binary package info: libibverbs1=40.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libibverbs1/40.0-1/binfiles?fileinfo=1 Get binary package info: libicu71=71.1-3 Binary URL: http://snapshot.notset.fr/mr/binary/libicu71/71.1-3/binfiles?fileinfo=1 Get binary package info: libidn2-0=2.3.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libidn2-0/2.3.3-1/binfiles?fileinfo=1 Get binary package info: libisl23=0.24-2 Binary URL: http://snapshot.notset.fr/mr/binary/libisl23/0.24-2/binfiles?fileinfo=1 Get binary package info: libitm1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libitm1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libjs-jquery=3.6.0+dfsg+~3.5.13-1 Binary URL: http://snapshot.notset.fr/mr/binary/libjs-jquery/3.6.0+dfsg+~3.5.13-1/binfiles?fileinfo=1 Get binary package info: libjs-jquery-ui=1.13.1+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/libjs-jquery-ui/1.13.1+dfsg-1/binfiles?fileinfo=1 Get binary package info: libjsoncpp25=1.9.5-4 Binary URL: http://snapshot.notset.fr/mr/binary/libjsoncpp25/1.9.5-4/binfiles?fileinfo=1 Get binary package info: libk5crypto3=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libk5crypto3/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: libkeyutils1=1.6.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libkeyutils1/1.6.3-1/binfiles?fileinfo=1 Get binary package info: libkrb5-3=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libkrb5-3/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: libkrb5support0=1.19.2-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/libkrb5support0/1.19.2-2+b2/binfiles?fileinfo=1 Get binary package info: libldap-2.5-0=2.5.12+dfsg-2 Binary URL: http://snapshot.notset.fr/mr/binary/libldap-2.5-0/2.5.12+dfsg-2/binfiles?fileinfo=1 Get binary package info: liblsan0=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/liblsan0/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libltdl-dev=2.4.7-4 Binary URL: http://snapshot.notset.fr/mr/binary/libltdl-dev/2.4.7-4/binfiles?fileinfo=1 Get binary package info: libltdl7=2.4.7-4 Binary URL: http://snapshot.notset.fr/mr/binary/libltdl7/2.4.7-4/binfiles?fileinfo=1 Get binary package info: liblz4-1=1.9.3-2 Binary URL: http://snapshot.notset.fr/mr/binary/liblz4-1/1.9.3-2/binfiles?fileinfo=1 Get binary package info: liblzma5=5.2.5-2.1 Binary URL: http://snapshot.notset.fr/mr/binary/liblzma5/5.2.5-2.1/binfiles?fileinfo=1 Get binary package info: libmagic-mgc=1:5.41-4 Binary URL: http://snapshot.notset.fr/mr/binary/libmagic-mgc/1:5.41-4/binfiles?fileinfo=1 Get binary package info: libmagic1=1:5.41-4 Binary URL: http://snapshot.notset.fr/mr/binary/libmagic1/1:5.41-4/binfiles?fileinfo=1 Get binary package info: libmd0=1.0.4-2 Binary URL: http://snapshot.notset.fr/mr/binary/libmd0/1.0.4-2/binfiles?fileinfo=1 Get binary package info: libmount1=2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/libmount1/2.38-4/binfiles?fileinfo=1 Get binary package info: libmpc3=1.2.1-2 Binary URL: http://snapshot.notset.fr/mr/binary/libmpc3/1.2.1-2/binfiles?fileinfo=1 Get binary package info: libmpfr6=4.1.0-3 Binary URL: http://snapshot.notset.fr/mr/binary/libmpfr6/4.1.0-3/binfiles?fileinfo=1 Get binary package info: libncurses6=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/libncurses6/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: libncursesw6=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/libncursesw6/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: libnettle8=3.7.3-1 Binary URL: http://snapshot.notset.fr/mr/binary/libnettle8/3.7.3-1/binfiles?fileinfo=1 Get binary package info: libnghttp2-14=1.47.0-1+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libnghttp2-14/1.47.0-1+b1/binfiles?fileinfo=1 Get binary package info: libnl-3-200=3.5.0-0.1 Binary URL: http://snapshot.notset.fr/mr/binary/libnl-3-200/3.5.0-0.1/binfiles?fileinfo=1 Get binary package info: libnl-3-dev=3.5.0-0.1 Binary URL: http://snapshot.notset.fr/mr/binary/libnl-3-dev/3.5.0-0.1/binfiles?fileinfo=1 Get binary package info: libnl-route-3-200=3.5.0-0.1 Binary URL: http://snapshot.notset.fr/mr/binary/libnl-route-3-200/3.5.0-0.1/binfiles?fileinfo=1 Get binary package info: libnl-route-3-dev=3.5.0-0.1 Binary URL: http://snapshot.notset.fr/mr/binary/libnl-route-3-dev/3.5.0-0.1/binfiles?fileinfo=1 Get binary package info: libnsl-dev=1.3.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libnsl-dev/1.3.0-2/binfiles?fileinfo=1 Get binary package info: libnsl2=1.3.0-2 Binary URL: http://snapshot.notset.fr/mr/binary/libnsl2/1.3.0-2/binfiles?fileinfo=1 Get binary package info: libnuma-dev=2.0.14-3 Binary URL: http://snapshot.notset.fr/mr/binary/libnuma-dev/2.0.14-3/binfiles?fileinfo=1 Get binary package info: libnuma1=2.0.14-3 Binary URL: http://snapshot.notset.fr/mr/binary/libnuma1/2.0.14-3/binfiles?fileinfo=1 Get binary package info: libopenmpi-dev=4.1.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libopenmpi-dev/4.1.4-1/binfiles?fileinfo=1 Get binary package info: libopenmpi3=4.1.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libopenmpi3/4.1.4-1/binfiles?fileinfo=1 Get binary package info: libp11-kit0=0.24.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libp11-kit0/0.24.1-1/binfiles?fileinfo=1 Get binary package info: libpam-modules=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam-modules/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpam-modules-bin=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam-modules-bin/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpam-runtime=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam-runtime/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpam0g=1.4.0-13 Binary URL: http://snapshot.notset.fr/mr/binary/libpam0g/1.4.0-13/binfiles?fileinfo=1 Get binary package info: libpciaccess0=0.16-3 Binary URL: http://snapshot.notset.fr/mr/binary/libpciaccess0/0.16-3/binfiles?fileinfo=1 Get binary package info: libpcre2-8-0=10.40-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpcre2-8-0/10.40-1/binfiles?fileinfo=1 Get binary package info: libpcre3=2:8.39-14 Binary URL: http://snapshot.notset.fr/mr/binary/libpcre3/2:8.39-14/binfiles?fileinfo=1 Get binary package info: libperl5.34=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libperl5.34/5.34.0-5/binfiles?fileinfo=1 Get binary package info: libpipeline1=1.5.6-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpipeline1/1.5.6-1/binfiles?fileinfo=1 Get binary package info: libpmix-dev=4.1.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libpmix-dev/4.1.2-2/binfiles?fileinfo=1 Get binary package info: libpmix2=4.1.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libpmix2/4.1.2-2/binfiles?fileinfo=1 Get binary package info: libprocps8=2:3.3.17-7+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libprocps8/2:3.3.17-7+b1/binfiles?fileinfo=1 Get binary package info: libpsl5=0.21.0-1.2 Binary URL: http://snapshot.notset.fr/mr/binary/libpsl5/0.21.0-1.2/binfiles?fileinfo=1 Get binary package info: libpsm-infinipath1=3.3+20.604758e7-6.1 Binary URL: http://snapshot.notset.fr/mr/binary/libpsm-infinipath1/3.3+20.604758e7-6.1/binfiles?fileinfo=1 Get binary package info: libpsm2-2=11.2.185-1 Binary URL: http://snapshot.notset.fr/mr/binary/libpsm2-2/11.2.185-1/binfiles?fileinfo=1 Get binary package info: libquadmath0=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libquadmath0/12.1.0-5/binfiles?fileinfo=1 Get binary package info: librdmacm1=40.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/librdmacm1/40.0-1/binfiles?fileinfo=1 Get binary package info: librhash0=1.4.3-2 Binary URL: http://snapshot.notset.fr/mr/binary/librhash0/1.4.3-2/binfiles?fileinfo=1 Get binary package info: librtmp1=2.4+20151223.gitfa8646d.1-2+b2 Binary URL: http://snapshot.notset.fr/mr/binary/librtmp1/2.4+20151223.gitfa8646d.1-2+b2/binfiles?fileinfo=1 Get binary package info: libsasl2-2=2.1.28+dfsg-6 Binary URL: http://snapshot.notset.fr/mr/binary/libsasl2-2/2.1.28+dfsg-6/binfiles?fileinfo=1 Get binary package info: libsasl2-modules-db=2.1.28+dfsg-6 Binary URL: http://snapshot.notset.fr/mr/binary/libsasl2-modules-db/2.1.28+dfsg-6/binfiles?fileinfo=1 Get binary package info: libseccomp2=2.5.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libseccomp2/2.5.4-1/binfiles?fileinfo=1 Get binary package info: libselinux1=3.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libselinux1/3.4-1/binfiles?fileinfo=1 Get binary package info: libsemanage-common=3.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsemanage-common/3.4-1/binfiles?fileinfo=1 Get binary package info: libsemanage2=3.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsemanage2/3.4-1/binfiles?fileinfo=1 Get binary package info: libsepol2=3.4-2 Binary URL: http://snapshot.notset.fr/mr/binary/libsepol2/3.4-2/binfiles?fileinfo=1 Get binary package info: libsigsegv2=2.14-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsigsegv2/2.14-1/binfiles?fileinfo=1 Get binary package info: libsmartcols1=2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/libsmartcols1/2.38-4/binfiles?fileinfo=1 Get binary package info: libsqlite3-0=3.39.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsqlite3-0/3.39.1-1/binfiles?fileinfo=1 Get binary package info: libsqlite3-dev=3.39.1-1 Binary URL: http://snapshot.notset.fr/mr/binary/libsqlite3-dev/3.39.1-1/binfiles?fileinfo=1 Get binary package info: libssh2-1=1.10.0-3+b1 Binary URL: http://snapshot.notset.fr/mr/binary/libssh2-1/1.10.0-3+b1/binfiles?fileinfo=1 Get binary package info: libssl-dev=3.0.4-2 Binary URL: http://snapshot.notset.fr/mr/binary/libssl-dev/3.0.4-2/binfiles?fileinfo=1 Get binary package info: libssl3=3.0.4-2 Binary URL: http://snapshot.notset.fr/mr/binary/libssl3/3.0.4-2/binfiles?fileinfo=1 Get binary package info: libstdc++-11-dev=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libstdc++-11-dev/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libstdc++6=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libstdc++6/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libsub-override-perl=0.09-3 Binary URL: http://snapshot.notset.fr/mr/binary/libsub-override-perl/0.09-3/binfiles?fileinfo=1 Get binary package info: libsystemd0=251.2-8 Binary URL: http://snapshot.notset.fr/mr/binary/libsystemd0/251.2-8/binfiles?fileinfo=1 Get binary package info: libtasn1-6=4.18.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libtasn1-6/4.18.0-4/binfiles?fileinfo=1 Get binary package info: libtinfo6=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtinfo6/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: libtirpc-common=1.3.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc-common/1.3.2-2/binfiles?fileinfo=1 Get binary package info: libtirpc-dev=1.3.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc-dev/1.3.2-2/binfiles?fileinfo=1 Get binary package info: libtirpc3=1.3.2-2 Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc3/1.3.2-2/binfiles?fileinfo=1 Get binary package info: libtool=2.4.7-4 Binary URL: http://snapshot.notset.fr/mr/binary/libtool/2.4.7-4/binfiles?fileinfo=1 Get binary package info: libtsan0=11.3.0-4 Binary URL: http://snapshot.notset.fr/mr/binary/libtsan0/11.3.0-4/binfiles?fileinfo=1 Get binary package info: libtsan2=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libtsan2/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libubsan1=12.1.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/libubsan1/12.1.0-5/binfiles?fileinfo=1 Get binary package info: libuchardet0=0.0.7-1 Binary URL: http://snapshot.notset.fr/mr/binary/libuchardet0/0.0.7-1/binfiles?fileinfo=1 Get binary package info: libucx0=1.13.0~rc2-1 Binary URL: http://snapshot.notset.fr/mr/binary/libucx0/1.13.0~rc2-1/binfiles?fileinfo=1 Get binary package info: libudev1=251.2-8 Binary URL: http://snapshot.notset.fr/mr/binary/libudev1/251.2-8/binfiles?fileinfo=1 Get binary package info: libunistring2=1.0-1 Binary URL: http://snapshot.notset.fr/mr/binary/libunistring2/1.0-1/binfiles?fileinfo=1 Get binary package info: libuuid1=2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/libuuid1/2.38-4/binfiles?fileinfo=1 Get binary package info: libuv1=1.44.1-2 Binary URL: http://snapshot.notset.fr/mr/binary/libuv1/1.44.1-2/binfiles?fileinfo=1 Get binary package info: libx11-6=2:1.7.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/libx11-6/2:1.7.5-1/binfiles?fileinfo=1 Get binary package info: libx11-data=2:1.7.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/libx11-data/2:1.7.5-1/binfiles?fileinfo=1 Get binary package info: libxau6=1:1.0.9-1 Binary URL: http://snapshot.notset.fr/mr/binary/libxau6/1:1.0.9-1/binfiles?fileinfo=1 Get binary package info: libxcb1=1.14-3 Binary URL: http://snapshot.notset.fr/mr/binary/libxcb1/1.14-3/binfiles?fileinfo=1 Get binary package info: libxdmcp6=1:1.1.2-3 Binary URL: http://snapshot.notset.fr/mr/binary/libxdmcp6/1:1.1.2-3/binfiles?fileinfo=1 Get binary package info: libxext6=2:1.3.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/libxext6/2:1.3.4-1/binfiles?fileinfo=1 Get binary package info: libxml2=2.9.14+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/libxml2/2.9.14+dfsg-1/binfiles?fileinfo=1 Get binary package info: libxnvctrl0=470.129.06-1 Binary URL: http://snapshot.notset.fr/mr/binary/libxnvctrl0/470.129.06-1/binfiles?fileinfo=1 Get binary package info: libzstd1=1.5.2+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/libzstd1/1.5.2+dfsg-1/binfiles?fileinfo=1 Get binary package info: linux-libc-dev=5.18.5-1 Binary URL: http://snapshot.notset.fr/mr/binary/linux-libc-dev/5.18.5-1/binfiles?fileinfo=1 Get binary package info: login=1:4.11.1+dfsg1-2 Binary URL: http://snapshot.notset.fr/mr/binary/login/1:4.11.1+dfsg1-2/binfiles?fileinfo=1 Get binary package info: lsb-base=11.2 Binary URL: http://snapshot.notset.fr/mr/binary/lsb-base/11.2/binfiles?fileinfo=1 Get binary package info: m4=1.4.18-5 Binary URL: http://snapshot.notset.fr/mr/binary/m4/1.4.18-5/binfiles?fileinfo=1 Get binary package info: make=4.3-4.1 Binary URL: http://snapshot.notset.fr/mr/binary/make/4.3-4.1/binfiles?fileinfo=1 Get binary package info: man-db=2.10.2-1 Binary URL: http://snapshot.notset.fr/mr/binary/man-db/2.10.2-1/binfiles?fileinfo=1 Get binary package info: mawk=1.3.4.20200120-3.1 Binary URL: http://snapshot.notset.fr/mr/binary/mawk/1.3.4.20200120-3.1/binfiles?fileinfo=1 Get binary package info: mpi-default-dev=1.14 Binary URL: http://snapshot.notset.fr/mr/binary/mpi-default-dev/1.14/binfiles?fileinfo=1 Get binary package info: ncurses-base=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/ncurses-base/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: ncurses-bin=6.3+20220423-2 Binary URL: http://snapshot.notset.fr/mr/binary/ncurses-bin/6.3+20220423-2/binfiles?fileinfo=1 Get binary package info: ocl-icd-libopencl1=2.2.14-3 Binary URL: http://snapshot.notset.fr/mr/binary/ocl-icd-libopencl1/2.2.14-3/binfiles?fileinfo=1 Get binary package info: openmpi-bin=4.1.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/openmpi-bin/4.1.4-1/binfiles?fileinfo=1 Get binary package info: openmpi-common=4.1.4-1 Binary URL: http://snapshot.notset.fr/mr/binary/openmpi-common/4.1.4-1/binfiles?fileinfo=1 Get binary package info: openssh-client=1:9.0p1-1+b1 Binary URL: http://snapshot.notset.fr/mr/binary/openssh-client/1:9.0p1-1+b1/binfiles?fileinfo=1 Get binary package info: passwd=1:4.11.1+dfsg1-2 Binary URL: http://snapshot.notset.fr/mr/binary/passwd/1:4.11.1+dfsg1-2/binfiles?fileinfo=1 Get binary package info: patch=2.7.6-7 Binary URL: http://snapshot.notset.fr/mr/binary/patch/2.7.6-7/binfiles?fileinfo=1 Get binary package info: perl=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/perl/5.34.0-5/binfiles?fileinfo=1 Get binary package info: perl-base=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/perl-base/5.34.0-5/binfiles?fileinfo=1 Get binary package info: perl-modules-5.34=5.34.0-5 Binary URL: http://snapshot.notset.fr/mr/binary/perl-modules-5.34/5.34.0-5/binfiles?fileinfo=1 Get binary package info: pkg-config=0.29.2-1 Binary URL: http://snapshot.notset.fr/mr/binary/pkg-config/0.29.2-1/binfiles?fileinfo=1 Get binary package info: po-debconf=1.0.21+nmu1 Binary URL: http://snapshot.notset.fr/mr/binary/po-debconf/1.0.21+nmu1/binfiles?fileinfo=1 Get binary package info: procps=2:3.3.17-7+b1 Binary URL: http://snapshot.notset.fr/mr/binary/procps/2:3.3.17-7+b1/binfiles?fileinfo=1 Get binary package info: rpcsvc-proto=1.4.2-4 Binary URL: http://snapshot.notset.fr/mr/binary/rpcsvc-proto/1.4.2-4/binfiles?fileinfo=1 Get binary package info: sed=4.8-1 Binary URL: http://snapshot.notset.fr/mr/binary/sed/4.8-1/binfiles?fileinfo=1 Get binary package info: sensible-utils=0.0.17 Binary URL: http://snapshot.notset.fr/mr/binary/sensible-utils/0.0.17/binfiles?fileinfo=1 Get binary package info: sgml-base=1.30 Binary URL: http://snapshot.notset.fr/mr/binary/sgml-base/1.30/binfiles?fileinfo=1 Get binary package info: sysvinit-utils=3.03-1 Binary URL: http://snapshot.notset.fr/mr/binary/sysvinit-utils/3.03-1/binfiles?fileinfo=1 Get binary package info: tar=1.34+dfsg-1 Binary URL: http://snapshot.notset.fr/mr/binary/tar/1.34+dfsg-1/binfiles?fileinfo=1 Get binary package info: util-linux=2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/util-linux/2.38-4/binfiles?fileinfo=1 Get binary package info: util-linux-extra=2.38-4 Binary URL: http://snapshot.notset.fr/mr/binary/util-linux-extra/2.38-4/binfiles?fileinfo=1 Get binary package info: xz-utils=5.2.5-2.1 Binary URL: http://snapshot.notset.fr/mr/binary/xz-utils/5.2.5-2.1/binfiles?fileinfo=1 Get binary package info: zlib1g=1:1.2.11.dfsg-4 Binary URL: http://snapshot.notset.fr/mr/binary/zlib1g/1:1.2.11.dfsg-4/binfiles?fileinfo=1 Get binary package info: zlib1g-dev=1:1.2.11.dfsg-4 Binary URL: http://snapshot.notset.fr/mr/binary/zlib1g-dev/1:1.2.11.dfsg-4/binfiles?fileinfo=1 Remaining packages to be found: 253 Timestamp source (2 packages): deb http://snapshot.notset.fr/archive/debian/20220707T030959Z/ unstable main Remaining packages to be found: 7 Timestamp source (1 packages): deb http://snapshot.notset.fr/archive/debian/20220713T220842Z/ unstable main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220713T145608Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220611T030612Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220712T215953Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220419T024549Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220714T210818Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220511T030041Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220501T085721Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220620T031814Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211103T025035Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220703T032011Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220426T025843Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220521T151904Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220720T211439Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220509T030319Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220219T032615Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220531T025502Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220707T212059Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220405T031327Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220528T035722Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220706T025631Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220717T030141Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220711T084956Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210823T024636Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211205T025806Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220705T030342Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211223T031038Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210816T024705Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210901T090918Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220401T091035Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220714T091738Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210922T025414Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220414T030009Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220208T091208Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220623T092901Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220416T025423Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210927T025314Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220220T025720Z/ bookworm main Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20220312T025835Z/ bookworm main Remaining packages to be found: 2 Timestamp source (2 packages): deb http://snapshot.notset.fr/archive/debian/20220720T032429Z/ bookworm main New buildinfo file: /tmp/hyphy-2.5.40+dfsg-1e5zdk_fn/hyphy_2.5.40+dfsg-1_all.buildinfo env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser:all=3.122 autoconf:all=2.71-2 automake:all=1:1.16.5-1.3 autopoint:all=0.21-6 autotools-dev:all=20220109.1 base-files:amd64=12.2 base-passwd:amd64=3.5.52 bash:amd64=5.1-6.1 binutils:amd64=2.38.50.20220707-1 binutils-common:amd64=2.38.50.20220707-1 binutils-x86-64-linux-gnu:amd64=2.38.50.20220707-1 bsdextrautils:amd64=2.38-4 bsdutils:amd64=1:2.38-4 build-essential:amd64=12.9 bzip2:amd64=1.0.8-5 chrpath:amd64=0.16-2+b1 cmake:amd64=3.23.2-1 cmake-data:all=3.23.2-1 coreutils:amd64=8.32-4.1 cpp:amd64=4:11.2.0-2 cpp-11:amd64=11.3.0-4 cpp-12:amd64=12.1.0-5 dash:amd64=0.5.11+git20210903+057cd650a4ed-8 debconf:all=1.5.79 debhelper:all=13.8 debianutils:amd64=5.7-0.2 dh-autoreconf:all=20 dh-elpa-helper:all=2.0.10 dh-strip-nondeterminism:all=1.13.0-1 diffutils:amd64=1:3.7-5 dpkg:amd64=1.21.9 dpkg-dev:all=1.21.9 dwz:amd64=0.14-1 emacsen-common:all=3.0.4 file:amd64=1:5.41-4 findutils:amd64=4.9.0-3 g++:amd64=4:11.2.0-2 g++-11:amd64=11.3.0-4 gcc:amd64=4:11.2.0-2 gcc-11:amd64=11.3.0-4 gcc-11-base:amd64=11.3.0-4 gcc-12:amd64=12.1.0-5 gcc-12-base:amd64=12.1.0-5 gettext:amd64=0.21-6 gettext-base:amd64=0.21-6 gfortran-12:amd64=12.1.0-5 grep:amd64=3.7-1 groff-base:amd64=1.22.4-8 gzip:amd64=1.12-1 hostname:amd64=3.23 ibverbs-providers:amd64=40.0-1 init-system-helpers:all=1.64 intltool-debian:all=0.35.0+20060710.5 libacl1:amd64=2.3.1-1 libarchive-zip-perl:all=1.68-1 libarchive13:amd64=3.6.0-1 libasan6:amd64=11.3.0-4 libasan8:amd64=12.1.0-5 libatomic1:amd64=12.1.0-5 libattr1:amd64=1:2.5.1-1 libaudit-common:all=1:3.0.7-1 libaudit1:amd64=1:3.0.7-1+b1 libbinutils:amd64=2.38.50.20220707-1 libblkid1:amd64=2.38-4 libbrotli1:amd64=1.0.9-2+b3 libbsd0:amd64=0.11.6-1 libbz2-1.0:amd64=1.0.8-5 libc-bin:amd64=2.33-8 libc-dev-bin:amd64=2.33-8 libc6:amd64=2.33-8 libc6-dev:amd64=2.33-8 libcap-ng0:amd64=0.8.3-1 libcap2:amd64=1:2.44-1 libcbor0.8:amd64=0.8.0-2 libcc1-0:amd64=12.1.0-5 libcom-err2:amd64=1.46.5-2 libcrypt-dev:amd64=1:4.4.28-2 libcrypt1:amd64=1:4.4.28-2 libctf-nobfd0:amd64=2.38.50.20220707-1 libctf0:amd64=2.38.50.20220707-1 libcurl3-gnutls:amd64=7.84.0-2 libcurl4:amd64=7.84.0-2 libcurl4-gnutls-dev:amd64=7.84.0-2 libdb5.3:amd64=5.3.28+dfsg1-0.10 libdebconfclient0:amd64=0.263 libdebhelper-perl:all=13.8 libdpkg-perl:all=1.21.9 libedit2:amd64=3.1-20210910-1 libelf1:amd64=0.187-1 libevent-2.1-7:amd64=2.1.12-stable-5+b1 libevent-core-2.1-7:amd64=2.1.12-stable-5+b1 libevent-dev:amd64=2.1.12-stable-5+b1 libevent-extra-2.1-7:amd64=2.1.12-stable-5+b1 libevent-openssl-2.1-7:amd64=2.1.12-stable-5+b1 libevent-pthreads-2.1-7:amd64=2.1.12-stable-5+b1 libexpat1:amd64=2.4.8-1 libfabric1:amd64=1.11.0-3 libffi8:amd64=3.4.2-4 libfido2-1:amd64=1.11.0-1+b1 libfile-stripnondeterminism-perl:all=1.13.0-1 libgcc-11-dev:amd64=11.3.0-4 libgcc-12-dev:amd64=12.1.0-5 libgcc-s1:amd64=12.1.0-5 libgcrypt20:amd64=1.10.1-2 libgdbm-compat4:amd64=1.23-1 libgdbm6:amd64=1.23-1 libgfortran-12-dev:amd64=12.1.0-5 libgfortran5:amd64=12.1.0-5 libglib2.0-0:amd64=2.72.3-1 libgmp10:amd64=2:6.2.1+dfsg1-1 libgnutls30:amd64=3.7.6-2 libgomp1:amd64=12.1.0-5 libgpg-error0:amd64=1.45-2 libgprofng0:amd64=2.38.50.20220707-1 libgssapi-krb5-2:amd64=1.19.2-2+b2 libhogweed6:amd64=3.7.3-1 libhwloc-dev:amd64=2.8.0-1 libhwloc-plugins:amd64=2.8.0-1 libhwloc15:amd64=2.8.0-1 libibverbs-dev:amd64=40.0-1 libibverbs1:amd64=40.0-1 libicu71:amd64=71.1-3 libidn2-0:amd64=2.3.3-1 libisl23:amd64=0.24-2 libitm1:amd64=12.1.0-5 libjs-jquery:all=3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui:all=1.13.1+dfsg-1 libjsoncpp25:amd64=1.9.5-4 libk5crypto3:amd64=1.19.2-2+b2 libkeyutils1:amd64=1.6.3-1 libkrb5-3:amd64=1.19.2-2+b2 libkrb5support0:amd64=1.19.2-2+b2 libldap-2.5-0:amd64=2.5.12+dfsg-2 liblsan0:amd64=12.1.0-5 libltdl-dev:amd64=2.4.7-4 libltdl7:amd64=2.4.7-4 liblz4-1:amd64=1.9.3-2 liblzma5:amd64=5.2.5-2.1 libmagic-mgc:amd64=1:5.41-4 libmagic1:amd64=1:5.41-4 libmd0:amd64=1.0.4-2 libmount1:amd64=2.38-4 libmpc3:amd64=1.2.1-2 libmpfr6:amd64=4.1.0-3 libncurses6:amd64=6.3+20220423-2 libncursesw6:amd64=6.3+20220423-2 libnettle8:amd64=3.7.3-1 libnghttp2-14:amd64=1.47.0-1+b1 libnl-3-200:amd64=3.5.0-0.1 libnl-3-dev:amd64=3.5.0-0.1 libnl-route-3-200:amd64=3.5.0-0.1 libnl-route-3-dev:amd64=3.5.0-0.1 libnsl-dev:amd64=1.3.0-2 libnsl2:amd64=1.3.0-2 libnuma-dev:amd64=2.0.14-3 libnuma1:amd64=2.0.14-3 libopenmpi-dev:amd64=4.1.4-1 libopenmpi3:amd64=4.1.4-1 libp11-kit0:amd64=0.24.1-1 libpam-modules:amd64=1.4.0-13 libpam-modules-bin:amd64=1.4.0-13 libpam-runtime:all=1.4.0-13 libpam0g:amd64=1.4.0-13 libpciaccess0:amd64=0.16-3 libpcre2-8-0:amd64=10.40-1 libpcre3:amd64=2:8.39-14 libperl5.34:amd64=5.34.0-5 libpipeline1:amd64=1.5.6-1 libpmix-dev:amd64=4.1.2-2 libpmix2:amd64=4.1.2-2 libprocps8:amd64=2:3.3.17-7+b1 libpsl5:amd64=0.21.0-1.2 libpsm-infinipath1:amd64=3.3+20.604758e7-6.1 libpsm2-2:amd64=11.2.185-1 libquadmath0:amd64=12.1.0-5 librdmacm1:amd64=40.0-1 librhash0:amd64=1.4.3-2 librtmp1:amd64=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2:amd64=2.1.28+dfsg-6 libsasl2-modules-db:amd64=2.1.28+dfsg-6 libseccomp2:amd64=2.5.4-1 libselinux1:amd64=3.4-1 libsemanage-common:all=3.4-1 libsemanage2:amd64=3.4-1 libsepol2:amd64=3.4-2 libsigsegv2:amd64=2.14-1 libsmartcols1:amd64=2.38-4 libsqlite3-0:amd64=3.39.1-1 libsqlite3-dev:amd64=3.39.1-1 libssh2-1:amd64=1.10.0-3+b1 libssl-dev:amd64=3.0.4-2 libssl3:amd64=3.0.4-2 libstdc++-11-dev:amd64=11.3.0-4 libstdc++6:amd64=12.1.0-5 libsub-override-perl:all=0.09-3 libsystemd0:amd64=251.2-8 libtasn1-6:amd64=4.18.0-4 libtinfo6:amd64=6.3+20220423-2 libtirpc-common:all=1.3.2-2 libtirpc-dev:amd64=1.3.2-2 libtirpc3:amd64=1.3.2-2 libtool:all=2.4.7-4 libtsan0:amd64=11.3.0-4 libtsan2:amd64=12.1.0-5 libubsan1:amd64=12.1.0-5 libuchardet0:amd64=0.0.7-1 libucx0:amd64=1.13.0~rc2-1 libudev1:amd64=251.2-8 libunistring2:amd64=1.0-1 libuuid1:amd64=2.38-4 libuv1:amd64=1.44.1-2 libx11-6:amd64=2:1.7.5-1 libx11-data:all=2:1.7.5-1 libxau6:amd64=1:1.0.9-1 libxcb1:amd64=1.14-3 libxdmcp6:amd64=1:1.1.2-3 libxext6:amd64=2:1.3.4-1 libxml2:amd64=2.9.14+dfsg-1 libxnvctrl0:amd64=470.129.06-1 libzstd1:amd64=1.5.2+dfsg-1 linux-libc-dev:amd64=5.18.5-1 login:amd64=1:4.11.1+dfsg1-2 lsb-base:all=11.2 m4:amd64=1.4.18-5 make:amd64=4.3-4.1 man-db:amd64=2.10.2-1 mawk:amd64=1.3.4.20200120-3.1 mpi-default-dev:amd64=1.14 ncurses-base:all=6.3+20220423-2 ncurses-bin:amd64=6.3+20220423-2 ocl-icd-libopencl1:amd64=2.2.14-3 openmpi-bin:amd64=4.1.4-1 openmpi-common:all=4.1.4-1 openssh-client:amd64=1:9.0p1-1+b1 passwd:amd64=1:4.11.1+dfsg1-2 patch:amd64=2.7.6-7 perl:amd64=5.34.0-5 perl-base:amd64=5.34.0-5 perl-modules-5.34:all=5.34.0-5 pkg-config:amd64=0.29.2-1 po-debconf:all=1.0.21+nmu1 procps:amd64=2:3.3.17-7+b1 rpcsvc-proto:amd64=1.4.2-4 sed:amd64=4.8-1 sensible-utils:all=0.0.17 sgml-base:all=1.30 sysvinit-utils:amd64=3.03-1 tar:amd64=1.34+dfsg-1 util-linux:amd64=2.38-4 util-linux-extra:amd64=2.38-4 xz-utils:amd64=5.2.5-2.1 zlib1g:amd64=1:1.2.11.dfsg-4 zlib1g-dev:amd64=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220717T030141Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220717T030141Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220707T030959Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220713T220842Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220720T032429Z/ bookworm 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=2.5.40+dfsg-1 && mkdir -p /build/hyphy-q8VtkD && dpkg-source --no-check -x /*.dsc /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg && chown -R builduser:builduser /build/hyphy-q8VtkD" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1657872509" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/hyphy-q8VtkD /tmp/hyphy-2.5.40+dfsg-1e5zdk_fn bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220720T211439Z bookworm main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.yGLN8UoAwl 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.yGLN8UoAwl Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 401 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220720T211439Z bookworm/main amd64 libfakeroot amd64 1.29-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220720T211439Z bookworm/main amd64 fakeroot amd64 1.29-1 [87.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (1007 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 ... 4656 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.29-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.29-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.29-1_amd64.deb ... Unpacking fakeroot (1.29-1) ... Setting up libfakeroot:amd64 (1.29-1) ... Setting up fakeroot (1.29-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-8) ... 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/20220717T030141Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220717T030141Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220707T030959Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220713T220842Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220720T032429Z/ bookworm main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.yGLN8UoAwl Get:1 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm InRelease [130 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220707T030959Z unstable InRelease [165 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220713T220842Z unstable InRelease [165 kB] Get:4 http://snapshot.notset.fr/archive/debian/20220720T032429Z bookworm InRelease [157 kB] Ign:5 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main Sources Ign:6 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main amd64 Packages Ign:5 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main Sources Ign:6 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main amd64 Packages Ign:5 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main Sources Ign:6 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main amd64 Packages Get:5 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main Sources [12.1 MB] Get:6 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main amd64 Packages [11.5 MB] Ign:7 http://snapshot.notset.fr/archive/debian/20220707T030959Z unstable/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220713T220842Z unstable/main amd64 Packages Ign:9 http://snapshot.notset.fr/archive/debian/20220720T032429Z bookworm/main amd64 Packages Ign:7 http://snapshot.notset.fr/archive/debian/20220707T030959Z unstable/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220713T220842Z unstable/main amd64 Packages Ign:9 http://snapshot.notset.fr/archive/debian/20220720T032429Z bookworm/main amd64 Packages Ign:7 http://snapshot.notset.fr/archive/debian/20220707T030959Z unstable/main amd64 Packages Ign:8 http://snapshot.notset.fr/archive/debian/20220713T220842Z unstable/main amd64 Packages Ign:9 http://snapshot.notset.fr/archive/debian/20220720T032429Z bookworm/main amd64 Packages Get:7 http://snapshot.notset.fr/archive/debian/20220707T030959Z unstable/main amd64 Packages [12.5 MB] Get:8 http://snapshot.notset.fr/archive/debian/20220713T220842Z unstable/main amd64 Packages [12.5 MB] Get:9 http://snapshot.notset.fr/archive/debian/20220720T032429Z bookworm/main amd64 Packages [11.5 MB] Fetched 60.9 MB in 49s (1254 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.yGLN8UoAwl I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d hyphy=2.5.40+dfsg-1 && mkdir -p /build/hyphy-q8VtkD && dpkg-source --no-check -x /*.dsc /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg && chown -R builduser:builduser /build/hyphy-q8VtkD"' exec /tmp/mmdebstrap.yGLN8UoAwl 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 2624 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main hyphy 2.5.40+dfsg-1 (dsc) [2382 B] Get:2 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main hyphy 2.5.40+dfsg-1 (tar) [2605 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220717T030141Z bookworm/main hyphy 2.5.40+dfsg-1 (diff) [16.6 kB] Fetched 2624 kB in 2s (1244 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'hyphy_2.5.40+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting hyphy in /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg dpkg-source: info: unpacking hyphy_2.5.40+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.5.40+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_sqlite.patch dpkg-source: info: applying rm_arch_specific_flags.patch dpkg-source: info: applying set-zlib-after-setting-default-libs.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1657872509" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.yGLN8UoAwl dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.5.40+dfsg-1 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-q8VtkD/hyphy-2.5.40+dfsg' dh_auto_clean --builddirectory obj-avx dh_auto_clean --builddirectory obj-sse3 dh_auto_clean make[1]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+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-q8VtkD/hyphy-2.5.40+dfsg' dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set default 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 "7.84.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.39.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -pthread -fopenmp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu dh_auto_configure --builddirectory obj-avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF cd obj-avx && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_FMA3 -- Performing Test HAVE_FMA3 - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set default compiler flags to -fsigned-char -O3 -std=c++14 -mavx -mfma -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.84.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.39.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -mavx -mfma -pthread -fopenmp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx dh_auto_configure --builddirectory obj-sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF cd obj-sse3 && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set default 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 "7.84.0") /usr/lib/x86_64-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.39.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -msse3 -pthread -fopenmp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX -- Build files have been written to: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 make[1]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg' # convert a few ISO-8859-1 files to address national-encoding set -e \ ; for file in res/TemplateBatchFiles/PARRIS.bf res/TemplateBatchFiles/TemplateModels/MEC.mdl res/TemplateBatchFiles/TemplateModels/models.lst \ ; do iconv -f ISO-8859-1 -t UTF-8 < ${file} > "${file}.new" \ ; mv "${file}.new" "${file}" \ ; done dh_auto_build -- MP MPI cd obj-x86_64-linux-gnu && make -j10 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 make[2]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/_hyExecutionContext.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o [ 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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fstring.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o /usr/bin/c++ 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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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/list.cpp.o -MF 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-I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ 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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 -lz -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+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-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MP.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' [100%] Built target MP make[4]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' [ 0%] 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__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/_hyExecutionContext.cpp [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include 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-I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" 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-c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/formula_parsing_context.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF 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-Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -MF 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link 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-I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/variablecontainer.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o /usr/bin/c++ 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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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object 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CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/_hyExecutionContext.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o [ 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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma 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-I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/category.cpp.o -MF CMakeFiles/hyphy.dir/src/core/category.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o 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-Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/fisher_exact.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fstring.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF 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-D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -MF CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -MF CMakeFiles/hyphy.dir/src/core/nexus.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/ntuplestorage.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/operation.cpp.o -MF CMakeFiles/hyphy.dir/src/core/operation.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/site.cpp.o -MF CMakeFiles/hyphy.dir/src/core/site.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include 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-I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_ 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/trie.cpp.o -MF CMakeFiles/hyphy.dir/src/core/trie.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/trie.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variable.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variable.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variable.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/variablecontainer.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -MF CMakeFiles/hyphy.dir/src/new/scfg.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -MF CMakeFiles/hyphy.dir/src/mains/unix.cpp.o.d -o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat 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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 -lz -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx/CMakeFiles/MP.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' [100%] Built target MP make[4]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' /usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx/CMakeFiles 20 make -f CMakeFiles/Makefile2 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-I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/avllistx.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/avllistx_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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ 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CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/baseobj.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ 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CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o.d -o 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-Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/strings.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/time_difference.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w 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-Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_ 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/build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -MF 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link 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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 -lz /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lgomp -lpthread make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-avx 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/usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' /usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg 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-I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/_hyExecutionContext.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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/associative_list.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ 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/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/avllistxl.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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -MF 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -MF CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/category.cpp.o -MF CMakeFiles/hyphy.dir/src/core/category.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/category.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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_ 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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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -MF CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -MF CMakeFiles/hyphy.dir/src/core/nexus.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -MF 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-D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -MF CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/site.cpp.o -MF CMakeFiles/hyphy.dir/src/core/site.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/stack.cpp.o -MF CMakeFiles/hyphy.dir/src/core/stack.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/strings.cpp.o -MF CMakeFiles/hyphy.dir/src/core/strings.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -MF CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/topology.cpp.o -MF CMakeFiles/hyphy.dir/src/core/topology.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/topology.cpp [ 70%] Building CXX 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-Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/variablecontainer.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/vector.cpp.o -MF CMakeFiles/hyphy.dir/src/core/vector.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bayesgraph.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bayesgraph2.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -MF CMakeFiles/hyphy.dir/src/new/scfg.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib/mersenne_twister.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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CMakeFiles/hyphy.dir/src/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 -lz -lgomp -lpthread mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3/CMakeFiles/MP.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' [100%] Built target MP make[4]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' /usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' [ 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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/alignment.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o [ 10%] 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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" 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-D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -MF 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/strings.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib/mersenne_twister.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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__ -D__ZLIB__ -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/core/include -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/contrib -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/lib/Link -I/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/hyphy-q8VtkD/hyphy-2.5.40+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-q8VtkD/hyphy-2.5.40+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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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 -lz /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lgomp -lpthread make[5]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3' cd /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg 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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 -j10 install DESTDIR=/build/hyphy-q8VtkD/hyphy-2.5.40\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg -B/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ascidian_mtDNA.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ciliate.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Euplotid_Nuclear.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Flatworm_mtDNA.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Mold_mtDNA.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Vertebratemtdna.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Yeast_mtDNA.cod -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Equal -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Equal -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params. -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Equal -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/aa.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/codon.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/dinuc.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/nuc.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary/F81.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69 -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def -- Installing: 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/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteREL.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CleanGaps.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CleanStopCodons.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ClusterAnalysis.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonModelCompare.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonToProtein.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ConvertDataFile.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/DirectionalREL.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/DistanceMatrix.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/JC69 -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P_RV -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_MH -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_RV -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/T3P -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN84 -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93 -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93_RV -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance -- Installing: 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/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/queryTree.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/readIndexFile.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relratioBootstrap.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/selectModelParameters.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/data -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/data/brown.nuc -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/data/integrase_BDA.nex -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/data/p51.aa -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/share/hyphy/data/p51.nex -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/bin/hyphy -- Installing: /build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/bin/HYPHYMPI -- Set runtime path of "/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/debian/tmp/usr/bin/HYPHYMPI" to "" make[1]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install-indep make[1]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg' dh_install -i dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/hyphy/bin make[1]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg' debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/hyphy-q8VtkD/hyphy-2.5.40+dfsg' dh_installdocs -i make[1]: Leaving directory '/build/hyphy-q8VtkD/hyphy-2.5.40+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_2.5.40+dfsg-1_all.deb'. dpkg-genbuildinfo --build=all -O../hyphy_2.5.40+dfsg-1_all.buildinfo dpkg-genchanges --build=all -O../hyphy_2.5.40+dfsg-1_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-q8VtkD /tmp/hyphy-2.5.40+dfsg-1e5zdk_fn I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.yGLN8UoAwl... I: success in 835.7089 seconds md5: hyphy-common_2.5.40+dfsg-1_all.deb: OK sha1: hyphy-common_2.5.40+dfsg-1_all.deb: OK sha256: hyphy-common_2.5.40+dfsg-1_all.deb: OK Checksums: OK