I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 31 10:02:39 +14 2023 I: pbuilder-time-stamp: 1675108959 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hyphy_2.5.28+dfsg-3.dsc] I: copying [./hyphy_2.5.28+dfsg.orig.tar.xz] I: copying [./hyphy_2.5.28+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.vDsM1rwZ/trustedkeys.kbx': General error gpgv: Signature made Wed Mar 17 22:41:39 2021 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hyphy_2.5.28+dfsg-3.dsc dpkg-source: info: extracting hyphy in hyphy-2.5.28+dfsg dpkg-source: info: unpacking hyphy_2.5.28+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.5.28+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_sqlite.patch dpkg-source: info: applying rm_arch_specific_flags.patch dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/801372/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/801372/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/801372/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=9abce664e32a477f9858067c60a98190 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=801372 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.k8Lk95uq8p/pbuilderrc_KtXm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.k8Lk95uq8p/b2 --logfile b2/build.log hyphy_2.5.28+dfsg-3.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 2021 more -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jan 31 10:02 sh -> bash lrwxrwxrwx 1 root root 4 Jan 24 05:47 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 2021 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/801372/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, mpi-default-dev, libcurl4-gnutls-dev | libcurl4-dev, libssl-dev, libsqlite3-dev, pkg-config, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl4-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-10{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libcbor0{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-10-dev{a} libgfortran5{a} libglib2.0-0{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu67{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp24{a} libldap-2.4-2{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libncurses6{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2{a} libprocps8{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libucx0{a} libuv1{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libldap-common libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 110 newly installed, 0 to remove and 0 not upgraded. Need to get 57.8 MB of archives. After unpacking 220 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libfido2-1 amd64 1.6.0-2 [53.3 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 openssh-client amd64 1:8.4p1-5 [929 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libgfortran-10-dev amd64 10.2.1-6 [769 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 gfortran-10 amd64 10.2.1-6 [9447 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libibverbs1 amd64 33.2-1 [59.4 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 ibverbs-providers amd64 33.2-1 [253 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u1 [429 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [169 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 librdmacm1 amd64 33.2-1 [68.9 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libhwloc15 amd64 2.4.1+dfsg-1 [150 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libltdl7 amd64 2.4.6-15 [391 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libltdl-dev amd64 2.4.6-15 [162 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libhwloc-dev amd64 2.4.1+dfsg-1 [231 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libxnvctrl0 amd64 460.91.03-1 [26.9 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 ocl-icd-libopencl1 amd64 2.2.14-2 [42.5 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libhwloc-plugins amd64 2.4.1+dfsg-1 [21.4 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libibverbs-dev amd64 33.2-1 [487 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libpmix2 amd64 4.0.0-4.1 [552 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libucx0 amd64 1.10.1~rc1+really.1.10.0-1 [649 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libopenmpi3 amd64 4.1.0-10 [2370 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 openmpi-common all 4.1.0-10 [179 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libpmix-dev amd64 4.0.0-4.1 [655 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 openmpi-bin amd64 4.1.0-10 [238 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libopenmpi-dev amd64 4.1.0-10 [1192 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-dev amd64 3.34.1-3 [963 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libssl-dev amd64 1.1.1k-1+deb11u1 [1810 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get: 110 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Fetched 57.8 MB in 1s (40.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../001-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../003-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../005-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../006-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../007-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../008-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... 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Preparing to unpack .../015-libedit2_3.1-20191231-2+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-2+b1) ... Selecting previously unselected package libcbor0:amd64. Preparing to unpack .../016-libcbor0_0.5.0+dfsg-2_amd64.deb ... Unpacking libcbor0:amd64 (0.5.0+dfsg-2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../017-libfido2-1_1.6.0-2_amd64.deb ... Unpacking libfido2-1:amd64 (1.6.0-2) ... Selecting previously unselected package openssh-client. Preparing to unpack .../018-openssh-client_1%3a8.4p1-5_amd64.deb ... Unpacking openssh-client (1:8.4p1-5) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../019-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../020-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. 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Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../028-libxml2_2.9.10+dfsg-6.7_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../029-libarchive13_3.4.3-2+b1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../030-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../031-libsasl2-modules-db_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../032-libsasl2-2_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:amd64. 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Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../039-libexpat1_2.2.10-2_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2) ... Selecting previously unselected package libjsoncpp24:amd64. Preparing to unpack .../040-libjsoncpp24_1.9.4-4_amd64.deb ... Unpacking libjsoncpp24:amd64 (1.9.4-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../041-librhash0_1.4.1-2_amd64.deb ... Unpacking librhash0:amd64 (1.4.1-2) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../042-libuv1_1.40.0-2_amd64.deb ... Unpacking libuv1:amd64 (1.40.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../043-cmake_3.18.4-2+deb11u1_amd64.deb ... Unpacking cmake (3.18.4-2+deb11u1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../044-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../045-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../046-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../047-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../048-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../049-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../050-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../051-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../052-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package gettext. Preparing to unpack .../053-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../054-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../055-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../056-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../057-libgfortran5_10.2.1-6_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.1-6) ... Selecting previously unselected package libgfortran-10-dev:amd64. Preparing to unpack .../058-libgfortran-10-dev_10.2.1-6_amd64.deb ... Unpacking libgfortran-10-dev:amd64 (10.2.1-6) ... Selecting previously unselected package gfortran-10. Preparing to unpack .../059-gfortran-10_10.2.1-6_amd64.deb ... Unpacking gfortran-10 (10.2.1-6) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../060-libnl-3-200_3.4.0-1+b1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../061-libnl-route-3-200_3.4.0-1+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../062-libibverbs1_33.2-1_amd64.deb ... Unpacking libibverbs1:amd64 (33.2-1) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../063-ibverbs-providers_33.2-1_amd64.deb ... Unpacking ibverbs-providers:amd64 (33.2-1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../064-libcurl3-gnutls_7.74.0-1.3+deb11u1_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../065-libcurl4-gnutls-dev_7.74.0-1.3+deb11u1_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u1) ... Selecting previously unselected package libevent-2.1-7:amd64. Preparing to unpack .../066-libevent-2.1-7_2.1.12-stable-1_amd64.deb ... Unpacking libevent-2.1-7:amd64 (2.1.12-stable-1) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../067-libevent-core-2.1-7_2.1.12-stable-1_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.12-stable-1) ... Selecting previously unselected package libevent-extra-2.1-7:amd64. Preparing to unpack .../068-libevent-extra-2.1-7_2.1.12-stable-1_amd64.deb ... Unpacking libevent-extra-2.1-7:amd64 (2.1.12-stable-1) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../069-libevent-pthreads-2.1-7_2.1.12-stable-1_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1) ... Selecting previously unselected package libevent-openssl-2.1-7:amd64. Preparing to unpack .../070-libevent-openssl-2.1-7_2.1.12-stable-1_amd64.deb ... Unpacking libevent-openssl-2.1-7:amd64 (2.1.12-stable-1) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../071-libevent-dev_2.1.12-stable-1_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../072-libpsm-infinipath1_3.3+20.604758e7-6.1_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.1) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../073-libnuma1_2.0.12-1+b1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.12-1+b1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../074-libpsm2-2_11.2.185-1_amd64.deb ... Unpacking libpsm2-2 (11.2.185-1) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../075-librdmacm1_33.2-1_amd64.deb ... Unpacking librdmacm1:amd64 (33.2-1) ... Selecting previously unselected package libfabric1. Preparing to unpack .../076-libfabric1_1.11.0-2_amd64.deb ... Unpacking libfabric1 (1.11.0-2) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../077-libglib2.0-0_2.66.8-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.66.8-1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../078-libhwloc15_2.4.1+dfsg-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.4.1+dfsg-1) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../079-libnuma-dev_2.0.12-1+b1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.12-1+b1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../080-libltdl7_2.4.6-15_amd64.deb ... Unpacking libltdl7:amd64 (2.4.6-15) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../081-libltdl-dev_2.4.6-15_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.6-15) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../082-libhwloc-dev_2.4.1+dfsg-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.4.1+dfsg-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../083-libpciaccess0_0.16-1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.16-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../084-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../085-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../086-libxcb1_1.14-3_amd64.deb ... Unpacking libxcb1:amd64 (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../087-libx11-data_2%3a1.7.2-1_all.deb ... Unpacking libx11-data (2:1.7.2-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../088-libx11-6_2%3a1.7.2-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.7.2-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../089-libxext6_2%3a1.3.3-1.1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1.1) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../090-libxnvctrl0_460.91.03-1_amd64.deb ... Unpacking libxnvctrl0:amd64 (460.91.03-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../091-ocl-icd-libopencl1_2.2.14-2_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.2.14-2) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../092-libhwloc-plugins_2.4.1+dfsg-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.4.1+dfsg-1) ... Selecting previously unselected package libnl-3-dev:amd64. Preparing to unpack .../093-libnl-3-dev_3.4.0-1+b1_amd64.deb ... Unpacking libnl-3-dev:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-dev:amd64. Preparing to unpack .../094-libnl-route-3-dev_3.4.0-1+b1_amd64.deb ... Unpacking libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Selecting previously unselected package libibverbs-dev:amd64. Preparing to unpack .../095-libibverbs-dev_33.2-1_amd64.deb ... Unpacking libibverbs-dev:amd64 (33.2-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../096-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ... Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../097-libjs-jquery-ui_1.12.1+dfsg-8+deb11u1_all.deb ... Unpacking libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../098-libpmix2_4.0.0-4.1_amd64.deb ... Unpacking libpmix2:amd64 (4.0.0-4.1) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../099-libucx0_1.10.1~rc1+really.1.10.0-1_amd64.deb ... Unpacking libucx0:amd64 (1.10.1~rc1+really.1.10.0-1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../100-libopenmpi3_4.1.0-10_amd64.deb ... Unpacking libopenmpi3:amd64 (4.1.0-10) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../101-openmpi-common_4.1.0-10_all.deb ... Unpacking openmpi-common (4.1.0-10) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../102-zlib1g-dev_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Selecting previously unselected package libpmix-dev:amd64. Preparing to unpack .../103-libpmix-dev_4.0.0-4.1_amd64.deb ... Unpacking libpmix-dev:amd64 (4.0.0-4.1) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../104-openmpi-bin_4.1.0-10_amd64.deb ... Unpacking openmpi-bin (4.1.0-10) ... Selecting previously unselected package libopenmpi-dev:amd64. Preparing to unpack .../105-libopenmpi-dev_4.1.0-10_amd64.deb ... Unpacking libopenmpi-dev:amd64 (4.1.0-10) ... Selecting previously unselected package libsqlite3-dev:amd64. Preparing to unpack .../106-libsqlite3-dev_3.34.1-3_amd64.deb ... Unpacking libsqlite3-dev:amd64 (3.34.1-3) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../107-libssl-dev_1.1.1k-1+deb11u1_amd64.deb ... Unpacking libssl-dev:amd64 (1.1.1k-1+deb11u1) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../108-mpi-default-dev_1.13_amd64.deb ... Unpacking mpi-default-dev (1.13) ... Selecting previously unselected package pkg-config. Preparing to unpack .../109-pkg-config_0.29.2-1_amd64.deb ... Unpacking pkg-config (0.29.2-1) ... Setting up libexpat1:amd64 (2.2.10-2) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libpciaccess0:amd64 (0.16-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libcbor0:amd64 (0.5.0+dfsg-2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:amd64 (1.40.0-2) ... Setting up libsqlite3-dev:amd64 (3.34.1-3) ... Setting up libx11-data (2:1.7.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libssl-dev:amd64 (1.1.1k-1+deb11u1) ... Setting up libhwloc15:amd64 (2.4.1+dfsg-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libltdl7:amd64 (2.4.6-15) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libjsoncpp24:amd64 (1.9.4-4) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up libnuma1:amd64 (2.0.12-1+b1) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up ocl-icd-libopencl1:amd64 (2.2.14-2) ... Setting up librhash0:amd64 (1.4.1-2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libnl-3-200:amd64 (3.4.0-1+b1) ... Setting up libpsm2-2 (11.2.185-1) ... Setting up openmpi-common (4.1.0-10) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:amd64 (10.2.1-6) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up cmake-data (3.18.4-2+deb11u1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libfido2-1:amd64 (1.6.0-2) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up chrpath (0.16-2+b1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:amd64 (3.4.3-2+b1) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Setting up libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:amd64 (2.0.12-1+b1) ... Setting up libnl-route-3-200:amd64 (3.4.0-1+b1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libevent-dev (2.1.12-stable-1) ... Setting up gfortran-10 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libnl-3-dev:amd64 (3.4.0-1+b1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u1) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:amd64 (33.2-1) ... Setting up ibverbs-providers:amd64 (33.2-1) ... Setting up openssh-client (1:8.4p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (460.91.03-1) ... Setting up dh-autoreconf (20) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-15) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up libhwloc-dev:amd64 (2.4.1+dfsg-1) ... Setting up librdmacm1:amd64 (33.2-1) ... Setting up libucx0:amd64 (1.10.1~rc1+really.1.10.0-1) ... Setting up debhelper (13.3.4) ... Setting up libibverbs-dev:amd64 (33.2-1) ... Setting up libhwloc-plugins:amd64 (2.4.1+dfsg-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (4.0.0-4.1) ... Setting up libopenmpi3:amd64 (4.1.0-10) ... Setting up libpmix-dev:amd64 (4.0.0-4.1) ... Setting up openmpi-bin (4.1.0-10) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.0-10) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.13) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Name or service not known I: Running cd /build/hyphy-2.5.28+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hyphy_2.5.28+dfsg-3_source.changes dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.5.28+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' dh_auto_clean --builddirectory obj-avx dh_auto_clean --builddirectory obj-sse3 dh_auto_clean make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Set compiler flags to -fsigned-char -O3 -std=c++14 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.34.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so Node not installed; API documentation will not be generated -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -pthread -fopenmp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /build/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu dh_auto_configure --builddirectory obj-avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF cd obj-avx && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_FMA3 -- Performing Test HAVE_FMA3 - Success Set compiler flags to -fsigned-char -O3 -std=c++14 -mavx -mfma -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.34.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so Node not installed; API documentation will not be generated -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -mavx -mfma -pthread -fopenmp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /build/hyphy-2.5.28+dfsg/obj-avx dh_auto_configure --builddirectory obj-sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF cd obj-sse3 && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success Set compiler flags to -fsigned-char -O3 -std=c++14 -msse3 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.74.0") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.34.1 -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so Node not installed; API documentation will not be generated -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -std=c++14 -msse3 -pthread -fopenmp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR INSTALL_PREFIX -- Build files have been written to: /build/hyphy-2.5.28+dfsg/obj-sse3 make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' # convert a few ISO-8859-1 files to address national-encoding set -e \ ; for file in res/TemplateBatchFiles/PARRIS.bf res/TemplateBatchFiles/TemplateModels/MEC.mdl res/TemplateBatchFiles/TemplateModels/models.lst \ ; 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-I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/bayesgraph.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link 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/build/hyphy-2.5.28+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/dataset_filter_numeric.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/fisher_exact.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 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/build/hyphy-2.5.28+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include 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-D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include 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-D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/time_difference.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat 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CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-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__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ 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-I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/avllistxl.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include 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-I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include 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70%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree.cpp.o /usr/bin/c++ 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-D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ 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-I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/trie.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/variable.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat 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-I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi 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25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ 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CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ 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-D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/ntuplestorage.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 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CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_AVX_INTRINSICS -D_SLKP_USE_FMA3_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -mavx -mfma -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/stack.cpp [ 60%] Building CXX 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Scanning dependencies of target hyphy make[5]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/hyphy-2.5.28+dfsg/obj-sse3' [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 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CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object 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/build/hyphy-2.5.28+dfsg/src/core/ntuplestorage.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o /usr/bin/c++ 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-I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g 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CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX 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CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/bayesgraph2.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o /usr/bin/c++ 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -g -fopenmp -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/hyphy-2.5.28+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. 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CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/fisher_exact.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/formula.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/formula_parsing_context.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o /usr/bin/c++ 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-I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 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-Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/ntuplestorage.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat 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-w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/stack.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/strings.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w 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CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -w -Wno-int-to-pointer-cast -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/hyphy-2.5.28+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp 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-I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -Weffc++ -Wextra -Wall -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/hyphy-2.5.28+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include 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-D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -I/build/hyphy-2.5.28+dfsg/src/core/include -I/build/hyphy-2.5.28+dfsg/src/contrib -I/build/hyphy-2.5.28+dfsg/src/lib/Link -I/build/hyphy-2.5.28+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -std=c++14 -msse3 -w -pthread -g -fopenmp -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/hyphy-2.5.28+dfsg/src/mains/unix.cpp [100%] Linking CXX executable HYPHYMPI /usr/bin/cmake -E cmake_link_script CMakeFiles/HYPHYMPI.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/hyphy-2.5.28+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -fsigned-char -O3 -std=c++14 -msse3 -pthread -g CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -o HYPHYMPI -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib: -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lgomp -lpthread make[5]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-sse3' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/hyphy-2.5.28+dfsg/obj-sse3' cd /build/hyphy-2.5.28+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hyphy-2.5.28+dfsg /build/hyphy-2.5.28+dfsg /build/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-2.5.28+dfsg/obj-sse3 /build/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles/MPI.dir/DependInfo.cmake --color= Dependee 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Scanning dependencies of target MPI make[5]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-sse3' make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/build make[5]: Entering directory '/build/hyphy-2.5.28+dfsg/obj-sse3' make[5]: Nothing to be done for 'CMakeFiles/MPI.dir/build'. make[5]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-sse3' [100%] Built target MPI make[4]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-sse3' /usr/bin/cmake -E cmake_progress_start /build/hyphy-2.5.28+dfsg/obj-sse3/CMakeFiles 0 make[3]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-sse3' make[2]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-sse3' make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' set -e ; for SIMD in avx sse3 ; do \ if lscpu | grep -q ${SIMD} ; then \ find "obj-${SIMD}/" \ -not -path "*/CMakeFiles/*" \ -type f,l \ -executable \ -exec cp -v '{}' . \; && \ ./run_unit_tests.sh ; \ fi ; \ done 'obj-avx/HYPHYMPI' -> './HYPHYMPI' 'obj-avx/HYPHYMP' -> './HYPHYMP' 'obj-avx/hyphy' -> './hyphy' ./tests/hbltests/UnitTests/HBLCommands/Abs.bf ./tests/hbltests/UnitTests/HBLCommands/Add.bf ./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf ./tests/hbltests/UnitTests/HBLCommands/Arctan.bf ./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf ./tests/hbltests/UnitTests/HBLCommands/Beta.bf ./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf ./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf ./tests/hbltests/UnitTests/HBLCommands/Branchname.bf ./tests/hbltests/UnitTests/HBLCommands/CChi2.bf ./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/Call.bf ./tests/hbltests/UnitTests/HBLCommands/Caret.bf ./tests/hbltests/UnitTests/HBLCommands/Category.bf ./tests/hbltests/UnitTests/HBLCommands/Columns.bf ./tests/hbltests/UnitTests/HBLCommands/Continue.bf ./tests/hbltests/UnitTests/HBLCommands/Cos.bf ./tests/hbltests/UnitTests/HBLCommands/DataSet.bf ./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf ./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf ./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf ./tests/hbltests/UnitTests/HBLCommands/Divide.bf ./tests/hbltests/UnitTests/HBLCommands/Do.bf ./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf ./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf ./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf ./tests/hbltests/UnitTests/HBLCommands/Erf.bf ./tests/hbltests/UnitTests/HBLCommands/Eval.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf ./tests/hbltests/UnitTests/HBLCommands/Exp.bf ./tests/hbltests/UnitTests/HBLCommands/Export.bf ./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf ./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf ./tests/hbltests/UnitTests/HBLCommands/For.bf ./tests/hbltests/UnitTests/HBLCommands/Format.bf ./tests/hbltests/UnitTests/HBLCommands/Function.bf ./tests/hbltests/UnitTests/HBLCommands/Gamma.bf ./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf ./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf ./tests/hbltests/UnitTests/HBLCommands/GetString.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf ./tests/hbltests/UnitTests/HBLCommands/IBeta.bf ./tests/hbltests/UnitTests/HBLCommands/IGamma.bf ./tests/hbltests/UnitTests/HBLCommands/If.bf ./tests/hbltests/UnitTests/HBLCommands/Integrate.bf ./tests/hbltests/UnitTests/HBLCommands/Inverse.bf ./tests/hbltests/UnitTests/HBLCommands/JSON.bf ./tests/hbltests/UnitTests/HBLCommands/Join.bf ./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf ./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf ./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf ./tests/hbltests/UnitTests/HBLCommands/Log.bf ./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf ./tests/hbltests/UnitTests/HBLCommands/Max.bf ./tests/hbltests/UnitTests/HBLCommands/Min.bf ./tests/hbltests/UnitTests/HBLCommands/Model.bf ./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf ./tests/hbltests/UnitTests/HBLCommands/Random.bf ./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf ./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf ./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf ./tests/hbltests/UnitTests/HBLCommands/Return.bf ./tests/hbltests/UnitTests/HBLCommands/Rows.bf ./tests/hbltests/UnitTests/HBLCommands/Simplex.bf ./tests/hbltests/UnitTests/HBLCommands/Simplify.bf ./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf ./tests/hbltests/UnitTests/HBLCommands/Sin.bf ./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf ./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf ./tests/hbltests/UnitTests/HBLCommands/Subtract.bf ./tests/hbltests/UnitTests/HBLCommands/Tan.bf ./tests/hbltests/UnitTests/HBLCommands/Time.bf ./tests/hbltests/UnitTests/HBLCommands/TipCount.bf ./tests/hbltests/UnitTests/HBLCommands/TipName.bf ./tests/hbltests/UnitTests/HBLCommands/Topology.bf ./tests/hbltests/UnitTests/HBLCommands/Transpose.bf ./tests/hbltests/UnitTests/HBLCommands/Tree.bf ./tests/hbltests/UnitTests/HBLCommands/Type.bf ./tests/hbltests/UnitTests/HBLCommands/While.bf ./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf ./tests/hbltests/UnitTests/HBLCommands/assert.bf ./tests/hbltests/UnitTests/HBLCommands/break.bf ./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf ./tests/hbltests/UnitTests/HBLCommands/include.bf ./tests/hbltests/UnitTests/HBLCommands/lfunction.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf ./tests/hbltests/UnitTests/HBLCommands/namespace.bf \n\n------------------------ALL TEST PASSED------------------------------------\n 'obj-sse3/HYPHYMPI' -> './HYPHYMPI' 'obj-sse3/HYPHYMP' -> './HYPHYMP' 'obj-sse3/hyphy' -> './hyphy' ./tests/hbltests/UnitTests/HBLCommands/Abs.bf ./tests/hbltests/UnitTests/HBLCommands/Add.bf ./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf ./tests/hbltests/UnitTests/HBLCommands/Arctan.bf ./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf ./tests/hbltests/UnitTests/HBLCommands/Beta.bf ./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf ./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf ./tests/hbltests/UnitTests/HBLCommands/Branchname.bf ./tests/hbltests/UnitTests/HBLCommands/CChi2.bf ./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/Call.bf ./tests/hbltests/UnitTests/HBLCommands/Caret.bf ./tests/hbltests/UnitTests/HBLCommands/Category.bf ./tests/hbltests/UnitTests/HBLCommands/Columns.bf ./tests/hbltests/UnitTests/HBLCommands/Continue.bf ./tests/hbltests/UnitTests/HBLCommands/Cos.bf ./tests/hbltests/UnitTests/HBLCommands/DataSet.bf ./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf ./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf ./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf ./tests/hbltests/UnitTests/HBLCommands/Divide.bf ./tests/hbltests/UnitTests/HBLCommands/Do.bf ./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf ./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf ./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf ./tests/hbltests/UnitTests/HBLCommands/Erf.bf ./tests/hbltests/UnitTests/HBLCommands/Eval.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf ./tests/hbltests/UnitTests/HBLCommands/Exp.bf ./tests/hbltests/UnitTests/HBLCommands/Export.bf ./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf ./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf ./tests/hbltests/UnitTests/HBLCommands/For.bf ./tests/hbltests/UnitTests/HBLCommands/Format.bf ./tests/hbltests/UnitTests/HBLCommands/Function.bf ./tests/hbltests/UnitTests/HBLCommands/Gamma.bf ./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf ./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf ./tests/hbltests/UnitTests/HBLCommands/GetString.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf ./tests/hbltests/UnitTests/HBLCommands/IBeta.bf ./tests/hbltests/UnitTests/HBLCommands/IGamma.bf ./tests/hbltests/UnitTests/HBLCommands/If.bf ./tests/hbltests/UnitTests/HBLCommands/Integrate.bf ./tests/hbltests/UnitTests/HBLCommands/Inverse.bf ./tests/hbltests/UnitTests/HBLCommands/JSON.bf ./tests/hbltests/UnitTests/HBLCommands/Join.bf ./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf ./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf ./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf ./tests/hbltests/UnitTests/HBLCommands/Log.bf ./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf ./tests/hbltests/UnitTests/HBLCommands/Max.bf ./tests/hbltests/UnitTests/HBLCommands/Min.bf ./tests/hbltests/UnitTests/HBLCommands/Model.bf ./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf ./tests/hbltests/UnitTests/HBLCommands/Random.bf ./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf ./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf ./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf ./tests/hbltests/UnitTests/HBLCommands/Return.bf ./tests/hbltests/UnitTests/HBLCommands/Rows.bf ./tests/hbltests/UnitTests/HBLCommands/Simplex.bf ./tests/hbltests/UnitTests/HBLCommands/Simplify.bf ./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf ./tests/hbltests/UnitTests/HBLCommands/Sin.bf ./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf ./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf ./tests/hbltests/UnitTests/HBLCommands/Subtract.bf ./tests/hbltests/UnitTests/HBLCommands/Tan.bf ./tests/hbltests/UnitTests/HBLCommands/Time.bf ./tests/hbltests/UnitTests/HBLCommands/TipCount.bf ./tests/hbltests/UnitTests/HBLCommands/TipName.bf ./tests/hbltests/UnitTests/HBLCommands/Topology.bf ./tests/hbltests/UnitTests/HBLCommands/Transpose.bf ./tests/hbltests/UnitTests/HBLCommands/Tree.bf ./tests/hbltests/UnitTests/HBLCommands/Type.bf ./tests/hbltests/UnitTests/HBLCommands/While.bf ./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf ./tests/hbltests/UnitTests/HBLCommands/assert.bf ./tests/hbltests/UnitTests/HBLCommands/break.bf ./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf ./tests/hbltests/UnitTests/HBLCommands/include.bf ./tests/hbltests/UnitTests/HBLCommands/lfunction.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf ./tests/hbltests/UnitTests/HBLCommands/namespace.bf \n\n------------------------ALL TEST PASSED------------------------------------\n find "obj-x86_64-linux-gnu/" \ -not -path "*/CMakeFiles/*" \ -type f,l \ -executable \ -exec cp -v '{}' . \; 'obj-x86_64-linux-gnu/HYPHYMPI' -> './HYPHYMPI' 'obj-x86_64-linux-gnu/HYPHYMP' -> './HYPHYMP' 'obj-x86_64-linux-gnu/hyphy' -> './hyphy' ./run_unit_tests.sh ./tests/hbltests/UnitTests/HBLCommands/Abs.bf ./tests/hbltests/UnitTests/HBLCommands/Add.bf ./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf ./tests/hbltests/UnitTests/HBLCommands/Arctan.bf ./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf ./tests/hbltests/UnitTests/HBLCommands/Beta.bf ./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf ./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf ./tests/hbltests/UnitTests/HBLCommands/Branchname.bf ./tests/hbltests/UnitTests/HBLCommands/CChi2.bf ./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/Call.bf ./tests/hbltests/UnitTests/HBLCommands/Caret.bf ./tests/hbltests/UnitTests/HBLCommands/Category.bf ./tests/hbltests/UnitTests/HBLCommands/Columns.bf ./tests/hbltests/UnitTests/HBLCommands/Continue.bf ./tests/hbltests/UnitTests/HBLCommands/Cos.bf ./tests/hbltests/UnitTests/HBLCommands/DataSet.bf ./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf ./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf ./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf ./tests/hbltests/UnitTests/HBLCommands/Divide.bf ./tests/hbltests/UnitTests/HBLCommands/Do.bf ./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf ./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf ./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf ./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf ./tests/hbltests/UnitTests/HBLCommands/Erf.bf ./tests/hbltests/UnitTests/HBLCommands/Eval.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf ./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf ./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf ./tests/hbltests/UnitTests/HBLCommands/Exp.bf ./tests/hbltests/UnitTests/HBLCommands/Export.bf ./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf ./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf ./tests/hbltests/UnitTests/HBLCommands/For.bf ./tests/hbltests/UnitTests/HBLCommands/Format.bf ./tests/hbltests/UnitTests/HBLCommands/Function.bf ./tests/hbltests/UnitTests/HBLCommands/Gamma.bf ./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf ./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf ./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf ./tests/hbltests/UnitTests/HBLCommands/GetString.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf ./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf ./tests/hbltests/UnitTests/HBLCommands/IBeta.bf ./tests/hbltests/UnitTests/HBLCommands/IGamma.bf ./tests/hbltests/UnitTests/HBLCommands/If.bf ./tests/hbltests/UnitTests/HBLCommands/Integrate.bf ./tests/hbltests/UnitTests/HBLCommands/Inverse.bf ./tests/hbltests/UnitTests/HBLCommands/JSON.bf ./tests/hbltests/UnitTests/HBLCommands/Join.bf ./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf ./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf ./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf ./tests/hbltests/UnitTests/HBLCommands/Log.bf ./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf ./tests/hbltests/UnitTests/HBLCommands/Max.bf ./tests/hbltests/UnitTests/HBLCommands/Min.bf ./tests/hbltests/UnitTests/HBLCommands/Model.bf ./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf ./tests/hbltests/UnitTests/HBLCommands/Random.bf ./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf ./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf ./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf ./tests/hbltests/UnitTests/HBLCommands/Return.bf ./tests/hbltests/UnitTests/HBLCommands/Rows.bf ./tests/hbltests/UnitTests/HBLCommands/Simplex.bf ./tests/hbltests/UnitTests/HBLCommands/Simplify.bf ./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf ./tests/hbltests/UnitTests/HBLCommands/Sin.bf ./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf ./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf ./tests/hbltests/UnitTests/HBLCommands/Subtract.bf ./tests/hbltests/UnitTests/HBLCommands/Tan.bf ./tests/hbltests/UnitTests/HBLCommands/Time.bf ./tests/hbltests/UnitTests/HBLCommands/TipCount.bf ./tests/hbltests/UnitTests/HBLCommands/TipName.bf ./tests/hbltests/UnitTests/HBLCommands/Topology.bf ./tests/hbltests/UnitTests/HBLCommands/Transpose.bf ./tests/hbltests/UnitTests/HBLCommands/Tree.bf ./tests/hbltests/UnitTests/HBLCommands/Type.bf ./tests/hbltests/UnitTests/HBLCommands/While.bf ./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf ./tests/hbltests/UnitTests/HBLCommands/assert.bf ./tests/hbltests/UnitTests/HBLCommands/break.bf ./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf ./tests/hbltests/UnitTests/HBLCommands/include.bf ./tests/hbltests/UnitTests/HBLCommands/lfunction.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf ./tests/hbltests/UnitTests/HBLCommands/namespace.bf \n\n------------------------ALL TEST PASSED------------------------------------\n make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/hyphy-2.5.28\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hyphy-2.5.28+dfsg -B/build/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/p51.nex -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/p51.aa -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/integrase_BDA.nex -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/data/brown.nuc -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/files.lst -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/selectModelParameters.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relratioBootstrap.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/readIndexFile.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/queryTree.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper4.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper3.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/posteriors.ibf -- Installing: 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Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24 -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV -- Installing: 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/build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1 -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62 -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.dat -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Default -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/190 -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SimmondsAI.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SimilarityPlot.bf -- 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/build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_binary -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_aa -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93_RV -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93 -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN84 -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/T3P -- Installing: 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/build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69 -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary/F81.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/nuc.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/dinuc.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/codon.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/aa.bf -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Equal -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params. -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Equal -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Equal -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Yeast_mtDNA.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Vertebratemtdna.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Mold_mtDNA.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Flatworm_mtDNA.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Euplotid_Nuclear.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ciliate.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ascidian_mtDNA.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/bin/hyphy -- Installing: /build/hyphy-2.5.28+dfsg/debian/tmp/usr/bin/HYPHYMPI -- Set runtime path of "/build/hyphy-2.5.28+dfsg/debian/tmp/usr/bin/HYPHYMPI" to "" make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' dh_install -a chrpath --delete obj-*/HYPHYMPI mkdir -p debian/hyphy-mpi/usr/lib/hyphy/bin mkdir -p debian/hyphy-pt/usr/lib/hyphy/bin cp obj-avx/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/HYPHYMPI-avx cp obj-sse3/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/HYPHYMPI-sse3 cp obj-avx/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/hyphy-avx cp obj-sse3/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/hyphy-sse3 mv debian/hyphy-mpi/usr/bin/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/ mv debian/hyphy-pt/usr/bin/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/ cd /build/hyphy-2.5.28+dfsg/debian/hyphy-mpi/usr/bin && \ ln -s ../lib/hyphy/bin/simd-dispatch HYPHYMPI cd /build/hyphy-2.5.28+dfsg/debian/hyphy-pt/usr/bin && \ ln -s ../lib/hyphy/bin/simd-dispatch hyphy make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' dh_install -i dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/hyphy/bin make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' debian/rules override_dh_installdocs-arch make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' dh_installdocs -a for news in debian/NEWS.Debian.* ; do \ pkg=`echo ${news} | sed 's/.*NEWS.Debian.//'` ; \ cp -a ${news} debian/${pkg}/usr/share/doc/${pkg}/NEWS.Debian ; \ done make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/hyphy-2.5.28+dfsg' dh_installdocs -i make[1]: Leaving directory '/build/hyphy-2.5.28+dfsg' dh_installchangelogs -O--buildsystem=cmake dh_installexamples -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'hyphy-pt' in '../hyphy-pt_2.5.28+dfsg-3_amd64.deb'. dpkg-deb: building package 'hyphy-pt-dbgsym' in '../hyphy-pt-dbgsym_2.5.28+dfsg-3_amd64.deb'. dpkg-deb: building package 'hyphy-mpi' in '../hyphy-mpi_2.5.28+dfsg-3_amd64.deb'. dpkg-deb: building package 'hyphy-mpi-dbgsym' in '../hyphy-mpi-dbgsym_2.5.28+dfsg-3_amd64.deb'. dpkg-deb: building package 'hyphy-common' in '../hyphy-common_2.5.28+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hyphy_2.5.28+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/801372/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/801372/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/801372 and its subdirectories I: Current time: Tue Jan 31 10:09:32 +14 2023 I: pbuilder-time-stamp: 1675109372