I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 10 13:54:08 +14 2026
I: pbuilder-time-stamp: 1775778848
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: Copying source file
I: copying [hyphy_2.5.69+dfsg-1.dsc]
I: copying [./hyphy_2.5.69+dfsg.orig.tar.xz]
I: copying [./hyphy_2.5.69+dfsg-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.69+dfsg-1.dsc: unsupported subcommand
dpkg-source: info: extracting hyphy in hyphy-2.5.69+dfsg
dpkg-source: info: unpacking hyphy_2.5.69+dfsg.orig.tar.xz
dpkg-source: info: unpacking hyphy_2.5.69+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/1589494/tmp/hooks/D01_modify_environment starting
debug: Running on ionos5-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Apr 9 23:54 /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/1589494/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/1589494/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DIRSTACK=()
DISTRIBUTION=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=c7e0b36f29824a97b6ff5a4e285e22f0
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=1589494
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.qyyl5JEe/pbuilderrc_K4y1 --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.qyyl5JEe/b2 --logfile b2/build.log hyphy_2.5.69+dfsg-1.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1589494/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19800 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} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} krb5-multidev{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli-dev{a} libbrotli1{a} libcbor0.10{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{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} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{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} libopenmpi40{a} libp11-kit-dev{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libucx0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} netbase{a} nettle-dev{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-minimal{a} python3.13{a} python3.13-dev{a} python3.13-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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget xauth
0 packages upgraded, 184 newly installed, 0 to remove and 0 not upgraded.
Need to get 155 MB of archives. After unpacking 612 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-1 [28.1 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.9p2-1 [970 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 chrpath amd64 0.18-1 [13.5 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-1 [2268 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-1 [12.0 MB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 73 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 libgfortran-14-dev amd64 14.2.0-17 [879 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17 [11.7 MB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 gfortran-14 amd64 14.2.0-17 [14.0 kB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 55.0-1 [62.2 kB]
Get: 86 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 55.0-1 [351 kB]
Get: 87 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-21 [23.6 MB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.124-1 [8180 B]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.124-1 [38.9 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.124-1 [22.4 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-5+b1 [8882 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 55.0-1 [70.2 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB]
Get: 145 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.5.4-3 [415 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 libltdl-dev amd64 2.5.4-3 [167 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 libhwloc-dev amd64 2.12.0-1 [255 kB]
Get: 148 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB]
Get: 156 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB]
Get: 157 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.12.0-1 [18.1 kB]
Get: 158 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 55.0-1 [28.5 kB]
Get: 159 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 55.0-1 [43.3 kB]
Get: 160 http://deb.debian.org/debian trixie/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB]
Get: 161 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB]
Get: 162 http://deb.debian.org/debian trixie/main amd64 libibverbs-dev amd64 55.0-1 [648 kB]
Get: 163 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 164 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 165 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 166 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 167 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB]
Get: 168 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.6-3 [651 kB]
Get: 169 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB]
Get: 170 http://deb.debian.org/debian trixie/main amd64 libopenmpi40 amd64 5.0.7-1 [2365 kB]
Get: 171 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 5.0.7-1 [97.2 kB]
Get: 172 http://deb.debian.org/debian trixie/main amd64 libpmix-dev amd64 5.0.6-3 [3961 kB]
Get: 173 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 5.0.7-1 [189 kB]
Get: 174 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 5.0.7-1 [1089 kB]
Get: 175 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB]
Get: 176 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB]
Get: 177 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.2-1 [10.3 kB]
Get: 178 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.2-1 [1068 B]
Get: 179 http://deb.debian.org/debian trixie/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB]
Get: 180 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.18 [3372 B]
Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.2-1 [1048 B]
Get: 182 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB]
Get: 183 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-1 [26.1 kB]
Get: 184 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.2-1 [1068 B]
Fetched 155 MB in 9s (17.8 MB/s)
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Setting up libpython3.13-minimal:amd64 (3.13.2-1) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Setting up python3-minimal (3.13.2-1) ...
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Unpacking python3 (3.13.2-1) ...
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Current default time zone: 'Etc/UTC'
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update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up openmpi-bin (5.0.7-1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist
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Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/1589494/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/1589494/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/hyphy-2.5.69+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_2.5.69+dfsg-1_source.changes
dpkg-buildpackage: info: source package hyphy
dpkg-buildpackage: info: source version 2.5.69+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --buildsystem=cmake
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
dh_auto_clean --builddirectory obj-avx
dh_auto_clean --builddirectory obj-sse3
dh_auto_clean
make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+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-2.5.69+dfsg'
dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON ..
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- 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 -g
Set linker flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g
-- 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/x86_64-linux-gnu/libcurl.so (found version "8.12.1")
/usr/lib/x86_64-linux-gnu/libcurl.so
Node not installed; API documentation will not be generated
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
-- Checking for module 'sqlite3'
-- Found sqlite3, version 3.46.1
-- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.3.1", minimum required is "1.2.9")
/usr/share/hyphy
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.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 -g -fopenmp
CMake Warning (dev) at CMakeLists.txt:698 (add_custom_command):
The following keywords are not supported when using
add_custom_command(TARGET): DEPENDS.
Policy CMP0175 is not set: add_custom_command() rejects invalid arguments.
Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:701 (makeLink)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (2.7s)
-- 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-2.5.69+dfsg/obj-x86_64-linux-gnu
dh_auto_configure --builddirectory obj-avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF
cd obj-avx && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF ..
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
-- Performing Test HAVE_FMA3
-- Performing Test HAVE_FMA3 - Success
-- Performing Test HAVE_NEON_EXTENSIONS
-- Performing Test HAVE_NEON_EXTENSIONS - Failed
Set compiler flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -mavx2 -mfma -g
Set linker flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -mavx2 -mfma -g
-- 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/x86_64-linux-gnu/libcurl.so (found version "8.12.1")
/usr/lib/x86_64-linux-gnu/libcurl.so
Node not installed; API documentation will not be generated
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
-- Checking for module 'sqlite3'
-- Found sqlite3, version 3.46.1
-- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.3.1", minimum required is "1.2.9")
/usr/share/hyphy
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -mavx2 -mfma -g -fopenmp
CMake Warning (dev) at CMakeLists.txt:698 (add_custom_command):
The following keywords are not supported when using
add_custom_command(TARGET): DEPENDS.
Policy CMP0175 is not set: add_custom_command() rejects invalid arguments.
Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:701 (makeLink)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (12.5s)
-- Generating done (0.2s)
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-2.5.69+dfsg/obj-avx
dh_auto_configure --builddirectory obj-sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF
cd obj-sse3 && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF ..
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- 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 -g
Set linker flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g
-- 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/x86_64-linux-gnu/libcurl.so (found version "8.12.1")
/usr/lib/x86_64-linux-gnu/libcurl.so
Node not installed; API documentation will not be generated
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
-- Checking for module 'sqlite3'
-- Found sqlite3, version 3.46.1
-- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.3.1", minimum required is "1.2.9")
/usr/share/hyphy
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.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 -g -fopenmp
CMake Warning (dev) at CMakeLists.txt:698 (add_custom_command):
The following keywords are not supported when using
add_custom_command(TARGET): DEPENDS.
Policy CMP0175 is not set: add_custom_command() rejects invalid arguments.
Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:701 (makeLink)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (6.9s)
-- 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-2.5.69+dfsg/obj-sse3
make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
dh_auto_build -- MP MPI
cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.69+dfsg -B/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 MP
make[3]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.69+dfsg -B/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu/CMakeFiles 20
make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all
make[4]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend
make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.69+dfsg /build/reproducible-path/hyphy-2.5.69+dfsg /build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake "--color="
make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build
make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
[ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o
[ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o
[ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o
[ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -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_numeric.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/dataset_filter_numeric.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-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -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-2.5.69+dfsg/src/core/batchlanhelpers.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-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -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-2.5.69+dfsg/src/core/avllist.cpp
[ 15%] 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-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/constant.cpp
[ 15%] 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-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -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-2.5.69+dfsg/src/core/dataset.cpp
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o
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[ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o
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/usr/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-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -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-2.5.69+dfsg/src/core/avllistx_iterator.cpp
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[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o
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[ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o
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[ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o
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[ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o
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/usr/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-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -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-2.5.69+dfsg/src/core/variablecontainer.cpp
[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o
[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o
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[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o
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/usr/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-2.5.69+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.69+dfsg/src/new/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -g -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-2.5.69+dfsg/src/new/bayesgraph.cpp
[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o
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[ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o
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[ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o
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[ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o
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[ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o
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[ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.cpp.o
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[ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o
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[ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o
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[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o
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[ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o
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[ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o
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[ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o
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[ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o
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[ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o
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[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o
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[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o
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[ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o
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[ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o
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[ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o
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[ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o
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[ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o
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[100%] Linking CXX executable HYPHYMPI
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -Wl,--dependency-file=CMakeFiles/HYPHYMPI.dir/link.d CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/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/x86_64-linux-gnu/openmpi/lib: -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a
make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
[100%] Built target HYPHYMPI
make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend
make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
cd /build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.69+dfsg /build/reproducible-path/hyphy-2.5.69+dfsg /build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3 /build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3 /build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3/CMakeFiles/MPI.dir/DependInfo.cmake "--color="
make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/build
make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
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make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
[100%] Built target MPI
make[4]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3/CMakeFiles 0
make[3]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
make[2]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-sse3'
make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
set -e ; for SIMD in avx sse3 ; do \
if lscpu | grep -q ${SIMD} ; then \
find "obj-${SIMD}/" \
-not -path "*/CMakeFiles/*" \
-type f,l \
-executable \
-exec cp -v '{}' . \; && \
./run_unit_tests.sh ; \
fi ; \
done
'obj-avx/HYPHYMP' -> './HYPHYMP'
'obj-avx/hyphy' -> './hyphy'
'obj-avx/HYPHYMPI' -> './HYPHYMPI'
./tests/hbltests/UnitTests/HBLCommands/Abs.bf
./tests/hbltests/UnitTests/HBLCommands/Add.bf
./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf
./tests/hbltests/UnitTests/HBLCommands/Arctan.bf
./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf
./tests/hbltests/UnitTests/HBLCommands/Beta.bf
./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf
./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf
./tests/hbltests/UnitTests/HBLCommands/Branchname.bf
./tests/hbltests/UnitTests/HBLCommands/CChi2.bf
./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf
./tests/hbltests/UnitTests/HBLCommands/Call.bf
./tests/hbltests/UnitTests/HBLCommands/Caret.bf
./tests/hbltests/UnitTests/HBLCommands/Category.bf
./tests/hbltests/UnitTests/HBLCommands/Columns.bf
./tests/hbltests/UnitTests/HBLCommands/Continue.bf
./tests/hbltests/UnitTests/HBLCommands/Cos.bf
./tests/hbltests/UnitTests/HBLCommands/DataSet.bf
./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf
./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf
./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf
./tests/hbltests/UnitTests/HBLCommands/Divide.bf
./tests/hbltests/UnitTests/HBLCommands/Do.bf
./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf
./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf
./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf
./tests/hbltests/UnitTests/HBLCommands/Erf.bf
./tests/hbltests/UnitTests/HBLCommands/Eval.bf
./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf
./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf
./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf
./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf
./tests/hbltests/UnitTests/HBLCommands/Exp.bf
./tests/hbltests/UnitTests/HBLCommands/Export.bf
./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf
./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf
./tests/hbltests/UnitTests/HBLCommands/For.bf
./tests/hbltests/UnitTests/HBLCommands/Format.bf
./tests/hbltests/UnitTests/HBLCommands/Function.bf
./tests/hbltests/UnitTests/HBLCommands/Gamma.bf
./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf
./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf
./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf
./tests/hbltests/UnitTests/HBLCommands/GetString.bf
./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf
./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf
./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf
./tests/hbltests/UnitTests/HBLCommands/IBeta.bf
./tests/hbltests/UnitTests/HBLCommands/IGamma.bf
./tests/hbltests/UnitTests/HBLCommands/If.bf
./tests/hbltests/UnitTests/HBLCommands/Integrate.bf
./tests/hbltests/UnitTests/HBLCommands/Inverse.bf
./tests/hbltests/UnitTests/HBLCommands/JSON.bf
./tests/hbltests/UnitTests/HBLCommands/Join.bf
./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf
./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf
./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf
./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf
./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf
./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf
./tests/hbltests/UnitTests/HBLCommands/Log.bf
./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf
./tests/hbltests/UnitTests/HBLCommands/Max.bf
./tests/hbltests/UnitTests/HBLCommands/Min.bf
./tests/hbltests/UnitTests/HBLCommands/Model.bf
./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf
./tests/hbltests/UnitTests/HBLCommands/Random.bf
./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf
./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf
./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf
./tests/hbltests/UnitTests/HBLCommands/Return.bf
./tests/hbltests/UnitTests/HBLCommands/Rows.bf
./tests/hbltests/UnitTests/HBLCommands/Simplex.bf
./tests/hbltests/UnitTests/HBLCommands/Simplify.bf
./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf
./tests/hbltests/UnitTests/HBLCommands/Sin.bf
./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf
./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf
./tests/hbltests/UnitTests/HBLCommands/Subtract.bf
./tests/hbltests/UnitTests/HBLCommands/Tan.bf
./tests/hbltests/UnitTests/HBLCommands/Time.bf
./tests/hbltests/UnitTests/HBLCommands/TipCount.bf
./tests/hbltests/UnitTests/HBLCommands/TipName.bf
./tests/hbltests/UnitTests/HBLCommands/Topology.bf
./tests/hbltests/UnitTests/HBLCommands/Transpose.bf
./tests/hbltests/UnitTests/HBLCommands/Tree.bf
./tests/hbltests/UnitTests/HBLCommands/Type.bf
./tests/hbltests/UnitTests/HBLCommands/While.bf
./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf
./tests/hbltests/UnitTests/HBLCommands/assert.bf
./tests/hbltests/UnitTests/HBLCommands/break.bf
./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf
./tests/hbltests/UnitTests/HBLCommands/include.bf
./tests/hbltests/UnitTests/HBLCommands/lfunction.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf
./tests/hbltests/UnitTests/HBLCommands/namespace.bf
\n\n------------------------ALL TEST PASSED------------------------------------\n
'obj-sse3/HYPHYMP' -> './HYPHYMP'
'obj-sse3/hyphy' -> './hyphy'
'obj-sse3/HYPHYMPI' -> './HYPHYMPI'
./tests/hbltests/UnitTests/HBLCommands/Abs.bf
./tests/hbltests/UnitTests/HBLCommands/Add.bf
./tests/hbltests/UnitTests/HBLCommands/Ampersand.bf
./tests/hbltests/UnitTests/HBLCommands/Arctan.bf
./tests/hbltests/UnitTests/HBLCommands/BayesianGraphicalModel.bf
./tests/hbltests/UnitTests/HBLCommands/Beta.bf
./tests/hbltests/UnitTests/HBLCommands/BranchLength.bf
./tests/hbltests/UnitTests/HBLCommands/Branchcount.bf
./tests/hbltests/UnitTests/HBLCommands/Branchname.bf
./tests/hbltests/UnitTests/HBLCommands/CChi2.bf
./tests/hbltests/UnitTests/HBLCommands/CGammaDist.bf
./tests/hbltests/UnitTests/HBLCommands/Call.bf
./tests/hbltests/UnitTests/HBLCommands/Caret.bf
./tests/hbltests/UnitTests/HBLCommands/Category.bf
./tests/hbltests/UnitTests/HBLCommands/Columns.bf
./tests/hbltests/UnitTests/HBLCommands/Continue.bf
./tests/hbltests/UnitTests/HBLCommands/Cos.bf
./tests/hbltests/UnitTests/HBLCommands/DataSet.bf
./tests/hbltests/UnitTests/HBLCommands/DataSetFilter.bf
./tests/hbltests/UnitTests/HBLCommands/DeleteObject.bf
./tests/hbltests/UnitTests/HBLCommands/Differentiate.bf
./tests/hbltests/UnitTests/HBLCommands/Divide.bf
./tests/hbltests/UnitTests/HBLCommands/Do.bf
./tests/hbltests/UnitTests/HBLCommands/DoSQL.bf
./tests/hbltests/UnitTests/HBLCommands/Dollarsign.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleAmpersand.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleEquals.bf
./tests/hbltests/UnitTests/HBLCommands/DoubleVerticalBar.bf
./tests/hbltests/UnitTests/HBLCommands/Eigensystem.bf
./tests/hbltests/UnitTests/HBLCommands/Erf.bf
./tests/hbltests/UnitTests/HBLCommands/Eval.bf
./tests/hbltests/UnitTests/HBLCommands/ExclamationPoint.bf
./tests/hbltests/UnitTests/HBLCommands/ExclamationPointEquals.bf
./tests/hbltests/UnitTests/HBLCommands/ExecuteAFile.bf
./tests/hbltests/UnitTests/HBLCommands/ExecuteCommands.bf
./tests/hbltests/UnitTests/HBLCommands/Exp.bf
./tests/hbltests/UnitTests/HBLCommands/Export.bf
./tests/hbltests/UnitTests/HBLCommands/Ffunction.bf
./tests/hbltests/UnitTests/HBLCommands/FindRoot.bf
./tests/hbltests/UnitTests/HBLCommands/For.bf
./tests/hbltests/UnitTests/HBLCommands/Format.bf
./tests/hbltests/UnitTests/HBLCommands/Function.bf
./tests/hbltests/UnitTests/HBLCommands/Gamma.bf
./tests/hbltests/UnitTests/HBLCommands/GammaDist.bf
./tests/hbltests/UnitTests/HBLCommands/GetDataInfo.bf
./tests/hbltests/UnitTests/HBLCommands/GetInformation.bf
./tests/hbltests/UnitTests/HBLCommands/GetString.bf
./tests/hbltests/UnitTests/HBLCommands/Greaterthan.bf
./tests/hbltests/UnitTests/HBLCommands/Greaterthanorequalto.bf
./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf
./tests/hbltests/UnitTests/HBLCommands/IBeta.bf
./tests/hbltests/UnitTests/HBLCommands/IGamma.bf
./tests/hbltests/UnitTests/HBLCommands/If.bf
./tests/hbltests/UnitTests/HBLCommands/Integrate.bf
./tests/hbltests/UnitTests/HBLCommands/Inverse.bf
./tests/hbltests/UnitTests/HBLCommands/JSON.bf
./tests/hbltests/UnitTests/HBLCommands/Join.bf
./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf
./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf
./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf
./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf
./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf
./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf
./tests/hbltests/UnitTests/HBLCommands/Log.bf
./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf
./tests/hbltests/UnitTests/HBLCommands/Max.bf
./tests/hbltests/UnitTests/HBLCommands/Min.bf
./tests/hbltests/UnitTests/HBLCommands/Model.bf
./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf
./tests/hbltests/UnitTests/HBLCommands/Random.bf
./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf
./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf
./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf
./tests/hbltests/UnitTests/HBLCommands/Return.bf
./tests/hbltests/UnitTests/HBLCommands/Rows.bf
./tests/hbltests/UnitTests/HBLCommands/Simplex.bf
./tests/hbltests/UnitTests/HBLCommands/Simplify.bf
./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf
./tests/hbltests/UnitTests/HBLCommands/Sin.bf
./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf
./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf
./tests/hbltests/UnitTests/HBLCommands/Subtract.bf
./tests/hbltests/UnitTests/HBLCommands/Tan.bf
./tests/hbltests/UnitTests/HBLCommands/Time.bf
./tests/hbltests/UnitTests/HBLCommands/TipCount.bf
./tests/hbltests/UnitTests/HBLCommands/TipName.bf
./tests/hbltests/UnitTests/HBLCommands/Topology.bf
./tests/hbltests/UnitTests/HBLCommands/Transpose.bf
./tests/hbltests/UnitTests/HBLCommands/Tree.bf
./tests/hbltests/UnitTests/HBLCommands/Type.bf
./tests/hbltests/UnitTests/HBLCommands/While.bf
./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf
./tests/hbltests/UnitTests/HBLCommands/assert.bf
./tests/hbltests/UnitTests/HBLCommands/break.bf
./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf
./tests/hbltests/UnitTests/HBLCommands/include.bf
./tests/hbltests/UnitTests/HBLCommands/lfunction.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf
./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf
./tests/hbltests/UnitTests/HBLCommands/namespace.bf
\n\n------------------------ALL TEST PASSED------------------------------------\n
find "obj-x86_64-linux-gnu/" \
-not -path "*/CMakeFiles/*" \
-type f,l \
-executable \
-exec cp -v '{}' . \;
'obj-x86_64-linux-gnu/HYPHYMP' -> './HYPHYMP'
'obj-x86_64-linux-gnu/hyphy' -> './hyphy'
'obj-x86_64-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-2.5.69+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=cmake
dh_prep -O--buildsystem=cmake
dh_auto_install -O--buildsystem=cmake
cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/hyphy-2.5.69\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.69+dfsg -B/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Vertebratemtdna.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Flatworm_mtDNA.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ciliate.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Yeast_mtDNA.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Euplotid_Nuclear.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Mold_mtDNA.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ascidian_mtDNA.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TreeTools.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignShared.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SimilarityPlot.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CleanStopCodons.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AddABias.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GA_CHC.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MolClockAllRoots.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AAModelComparison.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/DistanceMatrix.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Gateaux.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ConvertDataFile.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN84
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_RV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/T3P
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P_RV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_MH
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93_RV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/JC69
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LHT.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LRTRecombTest.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/molclockBootstrap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/NucModelCompare.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MGvsGY.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/selectModelParameters.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LZ_Complexity.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/posteriors.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/readIndexFile.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GUI
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/categoryEcho.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_MFReader_.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CleanGaps.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/RelativeRatio.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SM-2019.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/PCH
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAF81
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/S4
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Default
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16A
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/190
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LEISR.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/NeighborJoining.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/last.date
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_tipDater.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ModelTest.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/stats.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/mapping.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/distances.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/all-terms.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/random.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary/empirical.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/protein.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_GTR.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/codon/MSS.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR-MutSel.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/function-loader.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BGM.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteREL.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PartitionDataFile.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonToProtein.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/UpperBound.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGIvL.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GARD.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/RelativeRate.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestClade.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionLRT.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/bayesgraph.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSequences.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/doSPRSwap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relratioBootstrap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/partitionSequences.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TopologySearch.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-joint-fitter.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestBranchDNDS.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-selector-2.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SandNSAmbigs.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-selector.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/files.lst
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestCladeMeans.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/KHTest.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MolecularClock.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGEmulator_MF.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SimmondsAI.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/WANC.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper3.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSites.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/FitnessAAModels.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LocalMolClock.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper4.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/PostScript.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/CodonTools.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/MPITools.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/NJ.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DBTools.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_CMS_Aux.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_BMS_Aux.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SequentialAddition.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/DirectionalREL.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SequentialAddition.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/doNNISwap.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/error-filter.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonModelCompare.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/NielsenYang.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GateauxMR.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGEmulator.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/globalChecker.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/binomial.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGASimProcessor.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/F_ST.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/chooseDistanceFormula.def
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/queryTree.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/sir.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/srs.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Samplers/lhc.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary/F81.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/codon.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/aa.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/dinuc.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/nuc.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Equal
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Equal
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Equal
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/data
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/data/brown.nuc
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/data/p51.aa
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/data/integrase_BDA.nex
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/data/p51.nex
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/bin/hyphy
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/bin/HYPHYMPI
-- Set non-toolchain portion of runtime path of "/build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/bin/HYPHYMPI" to ""
make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-x86_64-linux-gnu'
debian/rules override_dh_install-arch
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
# convert a few ISO-8859-1 files to address national-encoding
set -e \
; for file in /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl /build/reproducible-path/hyphy-2.5.69+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-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf.new' -> '/build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf'
renamed '/build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl.new' -> '/build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl'
renamed '/build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst.new' -> '/build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst'
dh_install -a
find -type f -name HYPHYMPI -exec chrpath --delete '{}' ';'
mkdir -p debian/hyphy-mpi/usr/lib/hyphy/bin
mkdir -p debian/hyphy-pt/usr/lib/hyphy/bin
cp obj-avx/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/HYPHYMPI-avx
cp obj-sse3/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/HYPHYMPI-sse3
cp obj-avx/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/hyphy-avx
cp obj-sse3/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/hyphy-sse3
mv debian/hyphy-mpi/usr/bin/HYPHYMPI debian/hyphy-mpi/usr/lib/hyphy/bin/
mv debian/hyphy-pt/usr/bin/hyphy debian/hyphy-pt/usr/lib/hyphy/bin/
cd /build/reproducible-path/hyphy-2.5.69+dfsg/debian/hyphy-mpi/usr/bin && \
ln -s ../lib/hyphy/bin/simd-dispatch HYPHYMPI
cd /build/reproducible-path/hyphy-2.5.69+dfsg/debian/hyphy-pt/usr/bin && \
ln -s ../lib/hyphy/bin/simd-dispatch hyphy
make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
debian/rules override_dh_install-indep
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
dh_install -i
dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/hyphy/bin
make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
debian/rules override_dh_installdocs-arch
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+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-2.5.69+dfsg'
debian/rules override_dh_installdocs-indep
make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
dh_installdocs -i
make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg'
dh_installchangelogs -O--buildsystem=cmake
dh_installexamples -O--buildsystem=cmake
dh_installman -O--buildsystem=cmake
dh_installsystemduser -O--buildsystem=cmake
dh_lintian -O--buildsystem=cmake
dh_perl -O--buildsystem=cmake
dh_link -O--buildsystem=cmake
dh_strip_nondeterminism -O--buildsystem=cmake
dh_compress -O--buildsystem=cmake
dh_fixperms -O--buildsystem=cmake
dh_missing -O--buildsystem=cmake
dh_dwz -a -O--buildsystem=cmake
dh_strip -a -O--buildsystem=cmake
dh_makeshlibs -a -O--buildsystem=cmake
dh_shlibdeps -a -O--buildsystem=cmake
dh_installdeb -O--buildsystem=cmake
dh_gencontrol -O--buildsystem=cmake
dh_md5sums -O--buildsystem=cmake
dh_builddeb -O--buildsystem=cmake
dpkg-deb: building package 'hyphy-pt-dbgsym' in '../hyphy-pt-dbgsym_2.5.69+dfsg-1_amd64.deb'.
dpkg-deb: building package 'hyphy-pt' in '../hyphy-pt_2.5.69+dfsg-1_amd64.deb'.
dpkg-deb: building package 'hyphy-mpi' in '../hyphy-mpi_2.5.69+dfsg-1_amd64.deb'.
dpkg-deb: building package 'hyphy-mpi-dbgsym' in '../hyphy-mpi-dbgsym_2.5.69+dfsg-1_amd64.deb'.
dpkg-deb: building package 'hyphy-common' in '../hyphy-common_2.5.69+dfsg-1_all.deb'.
dpkg-genbuildinfo --build=binary -O../hyphy_2.5.69+dfsg-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../hyphy_2.5.69+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/1589494/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/1589494/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/1589494 and its subdirectories
I: Current time: Fri Apr 10 13:58:01 +14 2026
I: pbuilder-time-stamp: 1775779081