I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 5 01:22:15 +14 2024 I: pbuilder-time-stamp: 1717500135 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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: using eatmydata during job I: Copying source file I: copying [hyphy_2.5.62+dfsg-1.dsc] I: copying [./hyphy_2.5.62+dfsg.orig.tar.xz] I: copying [./hyphy_2.5.62+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jun 2 08:58:33 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.62+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting hyphy in hyphy-2.5.62+dfsg dpkg-source: info: unpacking hyphy_2.5.62+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.5.62+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_sqlite.patch dpkg-source: info: applying rm_arch_specific_flags.patch dpkg-source: info: applying set-zlib-after-setting-default-libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/535/tmp/hooks/D01_modify_environment starting debug: Running on infom07-i386. 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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 4 11:22 /bin/sh -> /bin/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/535/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/535/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=2fd2de90488c4154a2b5b4098054f8de LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=535 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/r-b-build.2eGdJNLg/pbuilderrc_Ir63 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2eGdJNLg/b2 --logfile b2/build.log hyphy_2.5.62+dfsg-1.dsc' SUDO_GID=111 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 3 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/535/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: i386 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, pkgconf, libpython3-all-dev, python3-all-dev:any, 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 ... 19683 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 pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libpython3-all-dev; however: Package libpython3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev:any. 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-13{a} gfortran-13-i686-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libbsd0{a} libcbor0.10{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{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} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libtool{a} libuchardet0{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libldap-common libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget xauth 0 packages upgraded, 142 newly installed, 0 to remove and 0 not upgraded. Need to get 95.0 MB of archives. After unpacking 360 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.9-1 [1918 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.9-1 [1795 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 13 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.3-1 [2224 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-4 [65.4 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-4 [876 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3 [42.9 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.1-4 [100 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20240517-1 [97.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libcbor0.10 i386 0.10.2-1.1 [30.7 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libfido2-1 i386 1.14.0-1+b2 [87.4 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 36 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 openssh-client i386 1:9.7p1-5 [991 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 chrpath i386 0.16-2+b1 [17.5 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.2-2 [387 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-6 [20.5 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-6 [60.6 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.17+dfsg-1 [198 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.61.0-1+b1 [84.0 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.0-5 [225 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.8.0-1 [477 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libjsoncpp25 i386 1.9.5-6+b2 [89.2 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 librhash0 i386 1.4.3-3+b1 [143 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-4 [156 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.29.3-1 [2167 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 cmake i386 3.29.3-1+b2 [11.9 MB] Get: 62 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 68 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240330-1 [735 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libgfortran-13-dev i386 13.2.0-25 [783 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 gfortran-13-i686-linux-gnu i386 13.2.0-25 [11.2 MB] Get: 77 http://deb.debian.org/debian trixie/main i386 gfortran-13 i386 13.2.0-25 [12.8 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libnl-3-200 i386 3.7.0-0.3 [61.8 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libnl-route-3-200 i386 3.7.0-0.3 [193 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libibverbs1 i386 50.0-2+b1 [66.7 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 ibverbs-providers i386 50.0-2+b1 [377 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.8.0-1 [469 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.8.0-1 [593 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10 [194 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libevent-core-2.1-7t64 i386 2.1.12-stable-10 [140 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libevent-extra-2.1-7t64 i386 2.1.12-stable-10 [113 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libevent-pthreads-2.1-7t64 i386 2.1.12-stable-10 [54.1 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libevent-openssl-2.1-7t64 i386 2.1.12-stable-10 [61.7 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libevent-dev i386 2.1.12-stable-10 [324 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.2-1 [165 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.3 [177 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 librdmacm1t64 i386 50.0-2+b1 [76.0 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libfabric1 i386 1.17.0-3+b1 [540 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libhwloc15 i386 2.10.0-1+b1 [175 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libnuma1 i386 2.0.18-1 [23.5 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libnuma-dev i386 2.0.18-1 [38.3 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libltdl7 i386 2.4.7-7+b1 [395 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libltdl-dev i386 2.4.7-7+b1 [167 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libhwloc-dev i386 2.10.0-1+b1 [268 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libpciaccess0 i386 0.17-3+b1 [53.8 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libxnvctrl0 i386 535.171.04-1 [13.7 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 ocl-icd-libopencl1 i386 2.3.2-1+b1 [43.5 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libhwloc-plugins i386 2.10.0-1+b1 [18.4 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libnl-3-dev i386 3.7.0-0.3 [105 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libnl-route-3-dev i386 3.7.0-0.3 [223 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libibverbs-dev i386 50.0-2+b1 [693 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.2.6-8 [150 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libopenmpi3t64 i386 4.1.6-13.3 [2626 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 openmpi-common all 4.1.6-13.3 [169 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 openmpi-bin i386 4.1.6-13.3 [198 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libopenmpi-dev i386 4.1.6-13.3 [1020 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-1+b2 [38.5 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libpython3.11t64 i386 3.11.9-1 [1982 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libpython3.11-dev i386 3.11.9-1 [4632 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.11.8-1 [9600 B] Get: 126 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.3-1 [1945 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 libpython3.12t64 i386 3.12.3-1 [2141 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.3-1 [5240 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libpython3-all-dev i386 3.11.8-1 [1068 B] Get: 130 http://deb.debian.org/debian trixie/main i386 libsqlite3-dev i386 3.45.3-1 [1173 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.2.1-3 [2744 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 mpi-default-dev i386 1.15 [3152 B] Get: 133 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.12.3-3.1 [131 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.3-1 [659 kB] Get: 138 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.11.8-1 [1056 B] Get: 139 http://deb.debian.org/debian trixie/main i386 python3.11-dev i386 3.11.9-1 [501 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.11.8-1 [26.1 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.3-1 [499 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 python3-all-dev i386 3.11.8-1 [1072 B] Fetched 95.0 MB in 1s (117 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19683 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.9-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_i386.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:i386 (3.11.9-1) ... Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 19999 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_i386.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../5-libreadline8t64_8.2-4_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_i386.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 20991 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_i386.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_i386.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../003-libproc2-0_2%3a4.0.4-4_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.4-4_i386.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. 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Unpacking libsasl2-2:i386 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../038-libldap-2.5-0_2.5.17+dfsg-1_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../039-libnghttp2-14_1.61.0-1+b1_i386.deb ... Unpacking libnghttp2-14:i386 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:i386. Preparing to unpack .../040-libpsl5t64_0.21.2-1.1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../041-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:i386. Preparing to unpack .../042-libssh2-1t64_1.11.0-5_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.0-5) ... Selecting previously unselected package libcurl4t64:i386. Preparing to unpack .../043-libcurl4t64_8.8.0-1_i386.deb ... Unpacking libcurl4t64:i386 (8.8.0-1) ... Selecting previously unselected package libjsoncpp25:i386. Preparing to unpack .../044-libjsoncpp25_1.9.5-6+b2_i386.deb ... Unpacking libjsoncpp25:i386 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:i386. Preparing to unpack .../045-librhash0_1.4.3-3+b1_i386.deb ... Unpacking librhash0:i386 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:i386. Preparing to unpack .../046-libuv1t64_1.48.0-4_i386.deb ... Unpacking libuv1t64:i386 (1.48.0-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../047-cmake-data_3.29.3-1_all.deb ... Unpacking cmake-data (3.29.3-1) ... Selecting previously unselected package cmake. Preparing to unpack .../048-cmake_3.29.3-1+b2_i386.deb ... Unpacking cmake (3.29.3-1+b2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../049-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../050-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../051-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../052-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../053-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../054-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/i386-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:i386 (1.11.0-5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:i386 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:i386 (13.2.0-25) ... Setting up libbsd0:i386 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Setting up chrpath (0.16-2+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up gfortran-13-i686-linux-gnu (13.2.0-25) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3+b1) ... Setting up libxcb1:i386 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:i386 (2.1.12-stable-10) ... Setting up libedit2:i386 (3.1-20240517-1) ... Setting up libevent-openssl-2.1-7t64:i386 (2.1.12-stable-10) ... Setting up libldap-2.5-0:i386 (2.5.17+dfsg-1) ... Setting up pkgconf:i386 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:i386 (2.0.18-1) ... Setting up libnl-route-3-200:i386 (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:i386 (2.4.7-7+b1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up gfortran-13 (13.2.0-25) ... Setting up libgssapi-krb5-2:i386 (1.20.1-6+b1) ... Setting up libjs-sphinxdoc (7.2.6-8) ... Setting up libevent-extra-2.1-7t64:i386 (2.1.12-stable-10) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libnl-3-dev:i386 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up libx11-6:i386 (2:1.8.7-1+b1) ... Setting up libhwloc-dev:i386 (2.10.0-1+b1) ... Setting up libarchive13t64:i386 (3.7.2-2) ... Setting up libibverbs1:i386 (50.0-2+b1) ... Setting up libpython3.12-stdlib:i386 (3.12.3-1) ... Setting up libcurl4t64:i386 (8.8.0-1) ... Setting up ibverbs-providers:i386 (50.0-2+b1) ... Setting up openssh-client (1:9.7p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:i386 (3.11.9-1) ... Setting up libcurl3t64-gnutls:i386 (8.8.0-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libcurl4-gnutls-dev:i386 (8.8.0-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:i386 (535.171.04-1) ... Setting up libpython3.12t64:i386 (3.12.3-1) ... Setting up libnl-route-3-dev:i386 (3.7.0-0.3) ... Setting up libpython3.11-dev:i386 (3.11.9-1) ... Setting up libevent-dev (2.1.12-stable-10) ... Setting up cmake (3.29.3-1+b2) ... Setting up librdmacm1t64:i386 (50.0-2+b1) ... Setting up libpython3-stdlib:i386 (3.11.8-1) ... Setting up libfabric1:i386 (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:i386 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:i386 (3.12.3-1) ... Setting up libibverbs-dev:i386 (50.0-2+b1) ... Setting up libhwloc-plugins:i386 (2.10.0-1+b1) ... Setting up libpython3-all-dev:i386 (3.11.8-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up libopenmpi3t64:i386 (4.1.6-13.3) ... Setting up python3-lib2to3 (3.12.3-3.1) ... Setting up openmpi-bin (4.1.6-13.3) ... 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 python3-distutils (3.12.3-3.1) ... python3.12: can't get files for byte-compilation Setting up python3-all (3.11.8-1) ... Setting up python3-dev (3.11.8-1) ... Setting up libopenmpi-dev:i386 (4.1.6-13.3) ... update-alternatives: using /usr/lib/i386-linux-gnu/openmpi/include to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up python3-all-dev (3.11.8-1) ... Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.38-11) ... 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 I: user script /srv/workspace/pbuilder/535/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/535/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/hyphy-2.5.62+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_2.5.62+dfsg-1_source.changes dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.5.62+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg' dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+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/reproducible-path/hyphy-2.5.62+dfsg' dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE4_EXTENSIONS -- Performing Test HAVE_SSE4_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 Set linker flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -- Could NOT find BLAS (missing: BLAS_LIBRARIES) -- 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/i386-linux-gnu/libcurl.so (found version "8.8.0") /usr/lib/i386-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.45.3 -- Found SQLITE3: /usr/lib/i386-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found suitable version "1.3.1", minimum required is "1.2.9") /usr/share/hyphy -- Found MPI_C: /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -fopenmp -- Configuring done (4.3s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED INSTALL_PREFIX NOSSE3 -- Build files have been written to: /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg' dh_auto_build -- MP MPI cd obj-i686-linux-gnu && make -j5 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.62+dfsg -B/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.62+dfsg -B/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/_hyExecutionContext.cpp [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/alignment.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/associative_list.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/avllistx_iterator.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/reproducible-path/hyphy-2.5.62+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_ 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-I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/batchlanhelpers.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ 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-I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS 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-I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/formula_parsing_context.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fstring.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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-D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/hyFile.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ 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-c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT 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-ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/matrix_mult.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -MF CMakeFiles/hyphy.dir/src/core/nexus.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ 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CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/ntuplestorage.cpp [ 55%] 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__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w 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-Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -MF CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/site.cpp.o 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/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT 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-std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/strings.cpp.o -MF CMakeFiles/hyphy.dir/src/core/strings.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/strings.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -MF CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/time_difference.cpp [ 70%] Building CXX object 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-I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie.cpp.o /usr/bin/c++ 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-I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/vector.cpp.o -MF CMakeFiles/hyphy.dir/src/core/vector.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/reproducible-path/hyphy-2.5.62+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\" 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/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib/mersenne_twister.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/mains/unix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -MF CMakeFiles/hyphy.dir/src/mains/unix.cpp.o.d -o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/mains/unix.cpp [100%] Linking CXX executable hyphy /usr/bin/cmake -E cmake_link_script CMakeFiles/hyphy.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o CMakeFiles/hyphy.dir/src/core/site.cpp.o CMakeFiles/hyphy.dir/src/core/stack.cpp.o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/hyphy.dir/src/core/strings.cpp.o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o CMakeFiles/hyphy.dir/src/core/topology.cpp.o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o CMakeFiles/hyphy.dir/src/core/tree.cpp.o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/trie.cpp.o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/variable.cpp.o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o CMakeFiles/hyphy.dir/src/core/vector.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -o hyphy -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 /usr/lib/i386-linux-gnu/libz.so /usr/lib/gcc/i686-linux-gnu/13/libgomp.so /usr/lib/i386-linux-gnu/libpthread.a mklink HYPHYMP -> hyphy ln -sf hyphy HYPHYMP make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' [100%] Built target hyphy make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/depend make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles/MP.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' [100%] Built target MP make[4]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.62+dfsg -B/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/alignment.cpp [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/_hyExecutionContext.cpp [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ 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-I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/avllistxl.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ 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CXX object CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -MF 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/batchlanhelpers.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c 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-D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/reproducible-path/hyphy-2.5.62+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__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/formula_parsing_context.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/global_things.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/hyFile.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -MF 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/matrix_mult.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/ntuplestorage.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/reproducible-path/hyphy-2.5.62+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_ 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/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT 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-I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/strings.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/variablecontainer.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/new/bayesgraph.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/new/bayesgraph2.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS 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/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.62+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/reproducible-path/hyphy-2.5.62+dfsg/src/mains/unix.cpp [100%] Linking CXX executable HYPHYMPI /usr/bin/cmake -E cmake_link_script CMakeFiles/HYPHYMPI.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.62+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 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 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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/matrix_mult.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/i386-linux-gnu/openmpi/lib: -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/i386-linux-gnu/openmpi/lib/libmpi.so /usr/lib/gcc/i686-linux-gnu/13/libgomp.so /usr/lib/i386-linux-gnu/libpthread.a make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles/MPI.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/build make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/MPI.dir/build'. make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' [100%] Built target MPI make[4]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg' find "obj-i686-linux-gnu/" \ -not -path "*/CMakeFiles/*" \ -type f,l \ -executable \ -exec cp -v '{}' . \; 'obj-i686-linux-gnu/hyphy' -> './hyphy' 'obj-i686-linux-gnu/HYPHYMP' -> './HYPHYMP' 'obj-i686-linux-gnu/HYPHYMPI' -> './HYPHYMPI' ./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/reproducible-path/hyphy-2.5.62+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-i686-linux-gnu && make -j5 install DESTDIR=/build/reproducible-path/hyphy-2.5.62\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.62+dfsg -B/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary/F81.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Equal -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Equal -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma -- Installing: 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/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/nuc.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/chooseDistanceFormula.def -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/molclockBootstrap.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignShared.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LocalMolClock.bf -- Installing: 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/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/NeighborJoining.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/WANC.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/sir.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/srs.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CleanStopCodons.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/CodonTools.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/NJ.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DBTools.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/GrabBag.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/PostScript.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/MPITools.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-selector.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/doNNISwap.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/KHTest.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/files.lst -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SandNSAmbigs.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestCladeMeans.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TreeTools.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.dat -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16A -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/S4 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAF81 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/190 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/PCH -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Default -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MolClockAllRoots.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SequentialAddition.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/queryTree.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GA_CHC.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSequences.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AddABias.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/partitionSequences.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSites.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGEmulator_MF.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN84 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_aa -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools.def -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/T3P -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_RV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P_RV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_MH -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/JC69 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_binary -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_codon -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93_RV -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93 -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/FitnessAAModels.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_tipDater.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/error-filter.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-selector-2.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ConvertDataFile.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/UpperBound.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_BMS_Aux.ibf -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Vertebratemtdna.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Euplotid_Nuclear.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Flatworm_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Yeast_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ascidian_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Mold_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ciliate.cod -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/data -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/data/brown.nuc -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/data/p51.aa -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/data/integrase_BDA.nex -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/data/p51.nex -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/bin/hyphy -- Installing: /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/bin/HYPHYMPI -- Set non-toolchain portion of runtime path of "/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/bin/HYPHYMPI" to "" make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg' # convert a few ISO-8859-1 files to address national-encoding set -e \ ; for file in /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl /build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst \ ; do iconv -f ISO-8859-1 -t UTF-8 < "${file}" > "${file}.new" \ ; mv -v "${file}.new" "${file}" \ ; done renamed '/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf.new' -> '/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf' renamed '/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl.new' -> '/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl' renamed '/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst.new' -> '/build/reproducible-path/hyphy-2.5.62+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst' dh_install -a chrpath --delete obj-*/HYPHYMPI make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg' dh_install -i make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+dfsg' debian/rules override_dh_installdocs-arch make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+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/reproducible-path/hyphy-2.5.62+dfsg' debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.62+dfsg' dh_installdocs -i make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.62+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-common' in '../hyphy-common_2.5.62+dfsg-1_all.deb'. dpkg-deb: building package 'hyphy-mpi-dbgsym' in '../hyphy-mpi-dbgsym_2.5.62+dfsg-1_i386.deb'. dpkg-deb: building package 'hyphy-mpi' in '../hyphy-mpi_2.5.62+dfsg-1_i386.deb'. dpkg-deb: building package 'hyphy-pt-dbgsym' in '../hyphy-pt-dbgsym_2.5.62+dfsg-1_i386.deb'. dpkg-deb: building package 'hyphy-pt' in '../hyphy-pt_2.5.62+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../hyphy_2.5.62+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../hyphy_2.5.62+dfsg-1_i386.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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/535/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/535/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/535 and its subdirectories I: Current time: Wed Jun 5 01:24:28 +14 2024 I: pbuilder-time-stamp: 1717500268