Thu Mar 6 09:51:57 UTC 2025 I: starting to build hyphy/unstable/armhf on jenkins on '2025-03-06 09:51'
Thu Mar 6 09:51:57 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_3/14085/console.log
Thu Mar 6 09:51:57 UTC 2025 I: Downloading source for unstable/hyphy=2.5.69+dfsg-1
--2025-03-06 09:51:57-- http://deb.debian.org/debian/pool/main/h/hyphy/hyphy_2.5.69%2bdfsg-1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2421 (2.4K) [text/prs.lines.tag]
Saving to: ‘hyphy_2.5.69+dfsg-1.dsc’
0K .. 100% 258M=0s
2025-03-06 09:51:57 (258 MB/s) - ‘hyphy_2.5.69+dfsg-1.dsc’ saved [2421/2421]
Thu Mar 6 09:51:57 UTC 2025 I: hyphy_2.5.69+dfsg-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: hyphy
Binary: hyphy-pt, hyphy-mpi, hyphy-common
Architecture: any all
Version: 2.5.69+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>, Nilesh Patra <nilesh@debian.org>
Homepage: https://hyphy.org/
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/hyphy
Vcs-Git: https://salsa.debian.org/med-team/hyphy.git
Testsuite: autopkgtest
Build-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
Package-List:
hyphy-common deb science optional arch=all
hyphy-mpi deb science optional arch=any
hyphy-pt deb science optional arch=any
Checksums-Sha1:
a491b54f1ab7005e80328e66cf686181336df66a 2633436 hyphy_2.5.69+dfsg.orig.tar.xz
49d63112fc857ef658e02c82e03e3a1c065df037 17452 hyphy_2.5.69+dfsg-1.debian.tar.xz
Checksums-Sha256:
34ef5370a72a08a221cf28a88f7bed1615b42594baf00a1813c7d15b63aa6e44 2633436 hyphy_2.5.69+dfsg.orig.tar.xz
3b879a7e775266fab981d57100407cad3ae6d346f66d3b69be56b385488ea2ba 17452 hyphy_2.5.69+dfsg-1.debian.tar.xz
Files:
7a1e7afbab1b40d2f140920e04e51067 2633436 hyphy_2.5.69+dfsg.orig.tar.xz
0bd4a3fe59e99932b5df9e9818f39634 17452 hyphy_2.5.69+dfsg-1.debian.tar.xz
Dgit: 269a1243915c833e4db3febfbf3ea63c02cea2be debian archive/debian/2.5.69+dfsg-1 https://git.dgit.debian.org/hyphy
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Thu Mar 6 09:51:57 UTC 2025 I: Checking whether the package is not for us
Thu Mar 6 09:51:57 UTC 2025 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net.
Thu Mar 6 09:51:57 UTC 2025 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net.
Thu Mar 6 10:00:24 UTC 2025 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Wed Mar 5 21:52:05 -12 2025
I: pbuilder-time-stamp: 1741254725
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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/29960/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='b53e4f1d67b64d918955ffa31435c8d4'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='29960'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tX5jPBTX/pbuilderrc_t2nE --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tX5jPBTX/b1 --logfile b1/build.log hyphy_2.5.69+dfsg-1.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux ff4a 6.1.0-31-armmp-lpae #1 SMP Debian 6.1.128-1 (2025-02-07) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/29960/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: armhf
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 ... 19508 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-arm-linux-gnueabihf{a} groff-base{a} hwloc-nox{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libffi8{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} libhwloc-dev{a} libhwloc15{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjs-jquery{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} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpich-dev{a} libmpich12{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} libnuma-dev{a} libnuma1{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{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} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libslurm42t64{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} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} mpich{a} netbase{a} nettle-dev{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 libhwloc-plugins libldap-common libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 139 newly installed, 0 to remove and 0 not upgraded.
Need to get 74.3 MB of archives. After unpacking 252 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.13-minimal armhf 3.13.2-1 [845 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf python3.13-minimal armhf 3.13.2-1 [1842 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.13.2-2 [27.1 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 12.0.0 [28.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf libffi8 armhf 3.4.7-1 [20.3 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-6 [146 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf libpython3.13-stdlib armhf 3.13.2-1 [1853 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf python3.13 armhf 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.13.2-2 [10.1 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.13.2-2 [28.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf libproc2-0 armhf 2:4.0.4-7 [56.3 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf procps armhf 2:4.0.4-7 [866 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.23.1-1 [238 kB]
Get: 22 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.4-5 [84.9 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-7 [272 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf automake all 1:1.17-3 [862 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf autopoint all 0.23.1-1 [770 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf chrpath armhf 0.18-1 [12.6 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf cmake-data all 3.31.6-1 [2268 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-6 [9086 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b2 [605 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf libarchive13t64 armhf 3.7.4-1.1 [306 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b7 [284 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-4 [30.3 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-4 [75.8 kB]
Get: 41 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B]
Get: 42 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-4 [285 kB]
Get: 43 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-4 [116 kB]
Get: 44 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-1 [444 kB]
Get: 45 http://deb.debian.org/debian unstable/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-9 [18.5 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-9 [50.4 kB]
Get: 48 http://deb.debian.org/debian unstable/main armhf libldap2 armhf 2.6.9+dfsg-1 [167 kB]
Get: 49 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB]
Get: 50 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.8.0-1 [59.9 kB]
Get: 51 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB]
Get: 52 http://deb.debian.org/debian unstable/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB]
Get: 53 http://deb.debian.org/debian unstable/main armhf libtasn1-6 armhf 4.20.0-2 [44.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main armhf libgnutls30t64 armhf 3.8.9-2 [1382 kB]
Get: 55 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB]
Get: 56 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB]
Get: 57 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.12.1-3 [320 kB]
Get: 58 http://deb.debian.org/debian unstable/main armhf libjsoncpp26 armhf 1.9.6-3 [69.9 kB]
Get: 59 http://deb.debian.org/debian unstable/main armhf librhash1 armhf 1.4.5-1 [143 kB]
Get: 60 http://deb.debian.org/debian unstable/main armhf libuv1t64 armhf 1.50.0-2 [140 kB]
Get: 61 http://deb.debian.org/debian unstable/main armhf cmake armhf 3.31.6-1 [5909 kB]
Get: 62 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.2-1 [55.1 kB]
Get: 63 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 64 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-4 [539 kB]
Get: 65 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 66 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 67 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 68 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 69 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 70 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 71 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.23.1-1 [1560 kB]
Get: 72 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 73 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 74 http://deb.debian.org/debian unstable/main armhf debhelper all 13.24.1 [920 kB]
Get: 75 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-17 [263 kB]
Get: 76 http://deb.debian.org/debian unstable/main armhf libgfortran-14-dev armhf 14.2.0-17 [315 kB]
Get: 77 http://deb.debian.org/debian unstable/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-17 [8720 kB]
Get: 78 http://deb.debian.org/debian unstable/main armhf gfortran-14 armhf 14.2.0-17 [14.0 kB]
Get: 79 http://deb.debian.org/debian unstable/main armhf libhwloc15 armhf 2.12.0-1 [135 kB]
Get: 80 http://deb.debian.org/debian unstable/main armhf hwloc-nox armhf 2.12.0-1 [204 kB]
Get: 81 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-4 [52.6 kB]
Get: 82 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-4 [37.5 kB]
Get: 83 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-4 [37.3 kB]
Get: 84 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-4 [47.4 kB]
Get: 85 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-4 [126 kB]
Get: 86 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b7 [294 kB]
Get: 87 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.11.0-1 [127 kB]
Get: 88 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.11.0-1 [26.7 kB]
Get: 89 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.12.1-3 [316 kB]
Get: 90 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB]
Get: 91 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1+b1 [539 kB]
Get: 92 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.9-2 [446 kB]
Get: 93 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.9-2 [446 kB]
Get: 94 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB]
Get: 95 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-3 [208 kB]
Get: 96 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.20.0-2 [93.4 kB]
Get: 97 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-3 [328 kB]
Get: 98 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-3 [592 kB]
Get: 99 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10.1-1 [1314 kB]
Get: 100 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.9-2 [1337 kB]
Get: 101 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-4 [15.9 kB]
Get: 102 http://deb.debian.org/debian unstable/main armhf libldap-dev armhf 2.6.9+dfsg-1 [286 kB]
Get: 103 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB]
Get: 104 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB]
Get: 105 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB]
Get: 106 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB]
Get: 107 http://deb.debian.org/debian unstable/main armhf libnghttp3-dev armhf 1.8.0-1 [84.8 kB]
Get: 108 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls-dev armhf 1.11.0-1 [32.2 kB]
Get: 109 http://deb.debian.org/debian unstable/main armhf libngtcp2-dev armhf 1.11.0-1 [178 kB]
Get: 110 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB]
Get: 111 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB]
Get: 112 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB]
Get: 113 http://deb.debian.org/debian unstable/main armhf libssl-dev armhf 3.4.1-1 [2429 kB]
Get: 114 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB]
Get: 115 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-2 [326 kB]
Get: 116 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.12.1-3 [441 kB]
Get: 117 http://deb.debian.org/debian unstable/main armhf libexpat1-dev armhf 2.6.4-1 [140 kB]
Get: 118 http://deb.debian.org/debian unstable/main armhf libnuma1 armhf 2.0.18-1+b1 [18.9 kB]
Get: 119 http://deb.debian.org/debian unstable/main armhf libnuma-dev armhf 2.0.18-1+b1 [34.6 kB]
Get: 120 http://deb.debian.org/debian unstable/main armhf libltdl7 armhf 2.5.4-4 [413 kB]
Get: 121 http://deb.debian.org/debian unstable/main armhf libltdl-dev armhf 2.5.4-4 [165 kB]
Get: 122 http://deb.debian.org/debian unstable/main armhf libhwloc-dev armhf 2.12.0-1 [227 kB]
Get: 123 http://deb.debian.org/debian unstable/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 124 http://deb.debian.org/debian unstable/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 125 http://deb.debian.org/debian unstable/main armhf libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 126 http://deb.debian.org/debian unstable/main armhf libmpich12 armhf 4.2.1-5 [1417 kB]
Get: 127 http://deb.debian.org/debian unstable/main armhf libslurm42t64 armhf 24.11.1-1 [695 kB]
Get: 128 http://deb.debian.org/debian unstable/main armhf mpich armhf 4.2.1-5 [203 kB]
Get: 129 http://deb.debian.org/debian unstable/main armhf libmpich-dev armhf 4.2.1-5 [2269 kB]
Get: 130 http://deb.debian.org/debian unstable/main armhf libpython3.13 armhf 3.13.2-1 [1868 kB]
Get: 131 http://deb.debian.org/debian unstable/main armhf libpython3.13-dev armhf 3.13.2-1 [3788 kB]
Get: 132 http://deb.debian.org/debian unstable/main armhf libpython3-dev armhf 3.13.2-2 [10.3 kB]
Get: 133 http://deb.debian.org/debian unstable/main armhf libpython3-all-dev armhf 3.13.2-2 [1068 B]
Get: 134 http://deb.debian.org/debian unstable/main armhf libsqlite3-dev armhf 3.46.1-1 [1003 kB]
Get: 135 http://deb.debian.org/debian unstable/main armhf mpi-default-dev armhf 1.18 [3372 B]
Get: 136 http://deb.debian.org/debian unstable/main armhf python3-all armhf 3.13.2-2 [1044 B]
Get: 137 http://deb.debian.org/debian unstable/main armhf python3.13-dev armhf 3.13.2-1 [505 kB]
Get: 138 http://deb.debian.org/debian unstable/main armhf python3-dev armhf 3.13.2-2 [26.1 kB]
Get: 139 http://deb.debian.org/debian unstable/main armhf python3-all-dev armhf 3.13.2-2 [1064 B]
Fetched 74.3 MB in 5s (15.8 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:armhf.
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Unpacking libpython3.13-minimal:armhf (3.13.2-1) ...
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Setting up libpython3.13-minimal:armhf (3.13.2-1) ...
Setting up libexpat1:armhf (2.6.4-1) ...
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Selecting previously unselected package python3-minimal.
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Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:armhf.
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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:armhf (8.2-6) ...
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Setting up python3-minimal (3.13.2-2) ...
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Preparing to unpack .../000-python3_3.13.2-2_armhf.deb ...
Unpacking python3 (3.13.2-2) ...
Selecting previously unselected package libproc2-0:armhf.
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Unpacking libproc2-0:armhf (2:4.0.4-7) ...
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Selecting previously unselected package groff-base.
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Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:armhf.
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Selecting previously unselected package libkeyutils1:armhf.
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Unpacking libkeyutils1:armhf (1.6.3-4) ...
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Selecting previously unselected package libunistring5:armhf.
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Selecting previously unselected package libldap2:armhf.
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Unpacking libldap2:armhf (2.6.9+dfsg-1) ...
Selecting previously unselected package libnghttp2-14:armhf.
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Unpacking libjsoncpp26:armhf (1.9.6-3) ...
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Unpacking libdebhelper-perl (13.24.1) ...
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Unpacking libtool (2.5.4-4) ...
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Unpacking dh-autoreconf (20) ...
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Setting up file (1:5.45-3+b1) ...
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Setting up libkrb5support0:armhf (1.21.3-4) ...
Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-9) ...
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
Local time is now: Thu Mar 6 09:53:29 UTC 2025.
Universal Time is now: Thu Mar 6 09:53:29 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up autotools-dev (20220109.1) ...
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Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
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Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up libldap2:armhf (2.6.9+dfsg-1) ...
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Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libgfortran-14-dev:armhf (14.2.0-17) ...
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Setting up gettext (0.23.1-1) ...
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Setting up nettle-dev:armhf (3.10.1-1) ...
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Setting up hwloc-nox (2.12.0-1) ...
Setting up libidn2-0:armhf (2.3.7-2+b1) ...
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Setting up intltool-debian (0.35.0+20060710.6) ...
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Setting up libldap-dev:armhf (2.6.9+dfsg-1) ...
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Setting up libgssapi-krb5-2:armhf (1.21.3-4) ...
Setting up libssh2-1-dev:armhf (1.11.1-1) ...
Setting up libidn2-dev:armhf (2.3.7-2+b1) ...
Setting up libjs-sphinxdoc (8.1.3-5) ...
Setting up libreadline8t64:armhf (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up libhwloc-dev:armhf (2.12.0-1) ...
Setting up libarchive13t64:armhf (3.7.4-1.1) ...
Setting up libpython3.13-stdlib:armhf (3.13.2-1) ...
Setting up libp11-kit-dev:armhf (0.25.5-3) ...
Setting up libpython3-stdlib:armhf (3.13.2-2) ...
Setting up gfortran-14-arm-linux-gnueabihf (14.2.0-17) ...
Setting up libpython3.13:armhf (3.13.2-1) ...
Setting up libgnutls30t64:armhf (3.8.9-2) ...
Setting up libgnutls-openssl27t64:armhf (3.8.9-2) ...
Setting up libnghttp2-dev:armhf (1.64.0-1) ...
Setting up python3.13 (3.13.2-1) ...
Setting up mpich (4.2.1-5) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ...
Setting up python3 (3.13.2-2) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ...
Setting up libgnutls-dane0t64:armhf (3.8.9-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libgssrpc4t64:armhf (1.21.3-4) ...
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Setting up gfortran-14 (14.2.0-17) ...
Setting up libngtcp2-crypto-gnutls8:armhf (1.11.0-1) ...
Setting up libkadm5clnt-mit12:armhf (1.21.3-4) ...
Setting up libgnutls28-dev:armhf (3.8.9-2) ...
Setting up libpython3-dev:armhf (3.13.2-2) ...
Setting up libcurl4t64:armhf (8.12.1-3) ...
Setting up libkdb5-10t64:armhf (1.21.3-4) ...
Setting up python3.13-dev (3.13.2-1) ...
Setting up libcurl3t64-gnutls:armhf (8.12.1-3) ...
Setting up python3-all (3.13.2-2) ...
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Setting up libngtcp2-crypto-gnutls-dev:armhf (1.11.0-1) ...
Setting up libpython3-all-dev:armhf (3.13.2-2) ...
Setting up python3-dev (3.13.2-2) ...
Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libmpich-dev:armhf (4.2.1-5) ...
update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.18) ...
Setting up libkadm5srv-mit12:armhf (1.21.3-4) ...
Setting up cmake (3.31.6-1) ...
Setting up krb5-multidev:armhf (1.21.3-4) ...
Setting up python3-all-dev (3.13.2-2) ...
Setting up libkrb5-dev:armhf (1.21.3-4) ...
Setting up libcurl4-gnutls-dev:armhf (8.12.1-3) ...
Processing triggers for libc-bin (2.41-3) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/hyphy-2.5.69+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 armhf
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
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-arm-linux-gnueabihf && 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/arm-linux-gnueabihf -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 - Failed
-- 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 -g
Set linker flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/arm-linux-gnueabihf/libcurl.so (found version "8.12.1")
/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/libsqlite3.so
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found suitable version "1.3.1", minimum required is "1.2.9")
/usr/share/hyphy
-- Found MPI_C: /usr/lib/arm-linux-gnueabihf/mpich/lib/libmpich.so (found version "4.1")
-- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/mpich/lib/libmpichcxx.so (found version "4.1")
-- Found MPI: TRUE (found version "4.1")
-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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 (9.1s)
-- Generating done (0.3s)
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-arm-linux-gnueabihf
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-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.69+dfsg -B/build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf --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-arm-linux-gnueabihf'
/usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.69+dfsg -B/build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 20
make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all
make[4]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend
make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf'
cd /build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/hyphy.dir/DependInfo.cmake "--color="
make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build
make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.69+dfsg/obj-arm-linux-gnueabihf'
[ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o
[ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o
[ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/_hyExecutionContext.cpp
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/alignment.cpp
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/associative_list.cpp
[ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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
[ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/avllistx.cpp
[ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/avllistxl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/avllistxl.cpp
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/avllistxl_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/avllistxl_iterator.cpp
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/baseobj.cpp.o -MF CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/baseobj.cpp
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o
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[ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o
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[ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o
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[ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o
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[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o
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[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o
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[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o
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[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o
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[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/dataset_filter.cpp
[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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
[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/fisher_exact.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/fisher_exact.cpp
[ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/formula.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/formula.cpp
[ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/formula_parsing_context.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/formula_parsing_context.cpp
[ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o
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[ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o
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[ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o
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[ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o
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[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o
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[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o
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[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o
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[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o
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[ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o
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[ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o
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[ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o
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[ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o
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[ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o
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[ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o
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[ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o
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[ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o
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[ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o
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[ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o
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[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o
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[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/site.cpp.o
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[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o
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[ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o
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[ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o
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[ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/strings.cpp.o -MF CMakeFiles/hyphy.dir/src/core/strings.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/strings.cpp
[ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/time_difference.cpp.o -MF CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/time_difference.cpp
[ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/topology.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/topology.cpp.o -MF CMakeFiles/hyphy.dir/src/core/topology.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/topology.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/topology.cpp
[ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o
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[ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/tree.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/tree.cpp
[ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o
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[ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o
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[ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie.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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[ 85%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.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/bgm.cpp.o
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[ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/scfg.cpp.o
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[ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o
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[ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o
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[ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o
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[ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o
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[ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o
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[ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o
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[ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o
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[ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o
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[ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o
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[ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o
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[ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o
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[ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/dataset_filter.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/dataset_filter.cpp
[ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o
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[ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o
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[ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o
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[ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o
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[ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o
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[ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o
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[ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o
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[ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/hbl_env.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/hbl_env.cpp
[ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o
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[ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o
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[ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/likefunc2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/likefunc2.cpp
[ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/likefuncocl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/likefuncocl.cpp
[ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o
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[ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/mathobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/mathobj.cpp
[ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/matrix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/matrix.cpp
[ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/matrix_mult.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/matrix_mult.cpp
[ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o
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[ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o
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[ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o
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[ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o
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[ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o
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[ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o
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[ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o
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[ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o
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[ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/stack.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/stack.cpp
[ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/string_buffer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/string_buffer.cpp
[ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -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/string_file_wrapper.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/core/string_file_wrapper.cpp
[ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o
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[ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o
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[ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o
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[ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o
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[ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o
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[ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o
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[ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o
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[ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.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/bayesgraph2.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
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -g -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/new/bgm2.cpp
[ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o
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[ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -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/arm-linux-gnueabihf/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.69+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -g -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c /build/reproducible-path/hyphy-2.5.69+dfsg/src/utils/hyphyunixutils.cpp
[ 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/contrib/regex.cpp.o
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\n\n------------------------ALL TEST PASSED------------------------------------\n
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-- 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/GY94customF3x4.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/modelParameters.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.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/Default
-- 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/rtREV_F.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/Yang2000Distributions.def
-- 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/S4
-- 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/Custom_AA_empirical.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/MG94x2.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/RNAREV_1
-- 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/MEC.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/GY94.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/JTT
-- 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/HIVWithin
-- 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/VT
-- 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/EmpiricalAA/MtArt
-- 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/IAV
-- 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/HIVBetween
-- 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/cpREV
-- 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/rtREV
-- 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/TrN.mdl
-- 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/Dayhoff.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/NRM+Freqs.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/models.lst
-- 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/mtMAM_F.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/RNAEqualInput
-- 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/PCH
-- 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/MG94wAA.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_F.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/mtREV_24_F.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/MG94wAAF61multiple.mdl
-- 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/reducedREV.mdl
-- 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/F81_binary.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/EIAAFreq.mdl
-- 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/BranchSiteTemplate.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/JC69.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/mtREV.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/ECM.mdl
-- 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/RNAREV
-- 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/TemplateModels/rtREV.mdl
-- 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/MG94customF1x4.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/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/190
-- 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/fitness.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/custm4x4.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/GRM.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/RNA16SvH.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/modelParameters2.mdl
-- 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/chooseGeneticCode.def
-- 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/CF3x4.bf
-- 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/GY94w9.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/GA_CHC.ibf
-- 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/SimmondsAI.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/chooseDistanceFormula.def
-- 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/files.lst
-- 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/SandNSAmbigs.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/distanceMethodNPBootstrap.bf
-- 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/BGM.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/YangNielsenBranchSite2005.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/SeqAlignmentCodonShared.ibf
-- 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/NucModelCompare.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/posteriors.ibf
-- 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/readIndexFile.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/CleanGaps.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/bayesgraph.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/2RatesAnalyses
-- 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/PARRIS_M3.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/discreteGeneratorNoPS.bf
-- 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/gamma2.def
-- 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/MG94GY94xREV_PARRIS_syn3.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/2RatesAnalyses/PARRIS_syn3.def
-- 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_synvar.def
-- 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/GY94.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/binomial.ibf
-- 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/GA_CHC_Binary.ibf
-- 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/CodonModelCompare.bf
-- 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/SGEmulator.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/_CMS_Aux.ibf
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-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf
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-- 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/SelectionLRT.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/qndhelper1_mf.ibf
-- 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/UtilityFunctions.bf
-- Installing: /build/reproducible-path/hyphy-2.5.69+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/libv3/models
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-- 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/MG_REV_TRIP.bf
-- 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_GTR.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/codon/MG_REV_MH.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/matrix2dict_aux.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/gcpREV.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/matrices/JC69.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/HIV.ibf
-- 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/frequencies.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/model_functions.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/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/GTR-MutSel.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/rate_variation.bf
-- 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/parameters.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/libv3/convenience
-- 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/math.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/tasks
-- 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/bayesgraph.ibf
-- 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/estimators.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/genetic_code.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/trees.bf
-- 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/stats.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/CodonToProtein.bf
-- 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/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/ErrorEstimates.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/WhatsInTheMean.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/dSdN.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/Drosophilia_adh.nex
-- 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/Phylohandbook.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/BranchAPriori.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/NucleotideBiases.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/MergeSequences.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/SGASimProcessor.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/ProteinAnalyses
-- 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/plusF_helper.ibf
-- 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/ProteinAnalyses/relative_prot_rates.bf
-- 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/SeqAlignmentCodon.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/TopologySearch.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/AnalyzeCodonData.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/SingleBreakpointRecomb.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/dNdSResultProcessor.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/lhc-ErrorEst.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/lhc.bf
-- 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_supp.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/GARD.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/pairwiseDistanceEstimator.ibf
-- 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/BivariateCodonRateAnalysis.bf
-- 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/SelectionAnalyses
-- 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/BUSTED.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/RELAX.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/contrast-meme.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/SLAC.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/FEL.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/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/aBSREL.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/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/io_functions.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/MGvsGY.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/Gateaux.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/last.date
-- 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/SGEmulator_MF.bf
-- 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/Distances
-- 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/TN84
-- 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/K2P_RV
-- 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/TN93_RV
-- 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/CodonTools2.def
-- 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/JC69
-- 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/p_Distance
-- 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/TN93
-- 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/Unaligned_LZ
-- 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/p_Distance_binary
-- 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/p_Distance_aa
-- 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/RelativeRatio.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/MolClockAllRoots.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/PairwiseRelativeRate.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/CodonBivariateRateProcessor.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/globalChecker.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/AnalyzeNucProtData.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/dNdSBivariateRateAnalysis.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/Utility
-- 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/CoalescentPostProcessor.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/Utility/HXB2Mapper.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/TreeFunctions.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/LocalMGREVMLFreqs.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/BranchLengthFitters.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/DescriptiveStatistics.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/PS_Plotters.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/DBTools.ibf
-- 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/AAModelComparison.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/selectModelParameters.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/SimilarityPlot.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/dNdSDistributionComparison.bf
-- 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/SlidingWindowAnalysis.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/FitnessAAModels.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/ReduceDataSetMatrix.bf
-- 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/relative_nucleotide_rates.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/SGIvL.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/partitionSequences.ibf
-- 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/qndhelper2_mf.ibf
-- 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/TopologySearchConstrained.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/doSPRSwap.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/MSS-selector-2.bf
-- 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/Blepharisma_Nuclear.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/Yeast_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/Vertebratemtdna.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/Alt_Yeast_Nuclear.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/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/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/data
-- 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/share/hyphy/data/integrase_BDA.nex
-- 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/brown.nuc
-- 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/Nucleotide
-- 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/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/F81.mdl
-- 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/EFVEstimated.ibf
-- 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/JC69
-- 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/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/Aminoacid
-- 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/Dayhoff.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/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/Codon
-- 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/MG94xHKY85_3x4_2Rates.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/MG94xTN93_3x4.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/MG94_REV_3x4.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/MG94_HKY85x3_4.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/MG94xREV_3x4_DualRV_GDD.mdl
-- 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/SubstitutionClasses
-- 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/CodonEFV
-- 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/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/AAEFV
-- 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/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/Estimated
-- 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/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/Beta
-- 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/2 Bin 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/Heterogeneity/General Discrete
-- 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/NucEFV
-- 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/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/Estimated
-- 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/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-arm-linux-gnueabihf'
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 '{}' ';'
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
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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dpkg-shlibdeps: warning: debian/hyphy-pt/usr/bin/hyphy contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hyphy-mpi/usr/bin/HYPHYMPI contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -O--buildsystem=cmake
dh_gencontrol -O--buildsystem=cmake
dh_md5sums -O--buildsystem=cmake
dh_builddeb -O--buildsystem=cmake
dpkg-deb: building package 'hyphy-pt' in '../hyphy-pt_2.5.69+dfsg-1_armhf.deb'.
dpkg-deb: building package 'hyphy-mpi' in '../hyphy-mpi_2.5.69+dfsg-1_armhf.deb'.
dpkg-deb: building package 'hyphy-common' in '../hyphy-common_2.5.69+dfsg-1_all.deb'.
dpkg-deb: building package 'hyphy-pt-dbgsym' in '../hyphy-pt-dbgsym_2.5.69+dfsg-1_armhf.deb'.
dpkg-deb: building package 'hyphy-mpi-dbgsym' in '../hyphy-mpi-dbgsym_2.5.69+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../hyphy_2.5.69+dfsg-1_armhf.buildinfo
dpkg-genchanges --build=binary -O../hyphy_2.5.69+dfsg-1_armhf.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: 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/29960 and its subdirectories
I: Current time: Wed Mar 5 21:59:57 -12 2025
I: pbuilder-time-stamp: 1741255197
Thu Mar 6 10:00:26 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt64z-armhf-rb.debian.net.
Thu Mar 6 10:00:26 UTC 2025 I: Preparing to do remote build '2' on virt64z-armhf-rb.debian.net.
Thu Mar 6 10:04:48 UTC 2025 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net.
Thu Mar 6 10:04:51 UTC 2025 I: hyphy_2.5.69+dfsg-1_armhf.changes:
Format: 1.8
Date: Wed, 05 Mar 2025 12:43:12 +0100
Source: hyphy
Binary: hyphy-common hyphy-mpi hyphy-mpi-dbgsym hyphy-pt hyphy-pt-dbgsym
Architecture: all armhf
Version: 2.5.69+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
hyphy-common - Hypothesis testing using Phylogenies (common files)
hyphy-mpi - Hypothesis testing using Phylogenies (MPI version)
hyphy-pt - Hypothesis testing using Phylogenies (pthreads version)
Changes:
hyphy (2.5.69+dfsg-1) unstable; urgency=medium
.
* New upstream version 2.5.69+dfsg (no changes).
* rm_arch_specific_flags.patch: update to include NEON variants.
This is needed to fix illegal instruction errors seen in autopkgtest.
* d/rules: leave a note to build NEON SIMDe variants.
* d/control: declare compliance to standards version 4.7.2.
Checksums-Sha1:
a6e997ae039ae6ed82d7b21c396eff82d7f4c23b 611532 hyphy-common_2.5.69+dfsg-1_all.deb
0ff26826d080a3168294ffa23b26bb3df88c77e9 3249844 hyphy-mpi-dbgsym_2.5.69+dfsg-1_armhf.deb
a2fe6982f1ef643fd5a2017c9f06003269071480 786188 hyphy-mpi_2.5.69+dfsg-1_armhf.deb
a330acb0751a47b8422fe9e7517c0eb6e3fecffc 3187568 hyphy-pt-dbgsym_2.5.69+dfsg-1_armhf.deb
6c794110f18b3f218fa43a0718f058288841a292 769512 hyphy-pt_2.5.69+dfsg-1_armhf.deb
4eb2091c0844c5fd59292c74a6e927073872110c 9057 hyphy_2.5.69+dfsg-1_armhf.buildinfo
Checksums-Sha256:
0a9fb20f2c464c46b72bf4173225dc45f9321cb99a5831034d8f21d07c60796a 611532 hyphy-common_2.5.69+dfsg-1_all.deb
692a7784ed85a5f9581da8f43238d27b9366e4009258499feeb45ff7c856f651 3249844 hyphy-mpi-dbgsym_2.5.69+dfsg-1_armhf.deb
230befbde3d7325d441dbfdf6882c992a1e2710637d2898c302b4d519d0e9c93 786188 hyphy-mpi_2.5.69+dfsg-1_armhf.deb
f911afa20126c72f34b184181802c4faa656fd319fd0534e74ac8080f03b3f38 3187568 hyphy-pt-dbgsym_2.5.69+dfsg-1_armhf.deb
21b40937f90835251a02f6762bd2bc6e18550a0f61b71fb5d2c94fa3451e1fac 769512 hyphy-pt_2.5.69+dfsg-1_armhf.deb
8d8e7b4aaf6cd5f7049e28086abb750634584b30e04f3ec3976cf4a3261c28ac 9057 hyphy_2.5.69+dfsg-1_armhf.buildinfo
Files:
839e8f3c74a663aa99f7c67f49b9e675 611532 science optional hyphy-common_2.5.69+dfsg-1_all.deb
0c0794ca69e66c5bd282876f6aa9fbe3 3249844 debug optional hyphy-mpi-dbgsym_2.5.69+dfsg-1_armhf.deb
fedd2dcc8d3284b6cbf3277fe7ccfd66 786188 science optional hyphy-mpi_2.5.69+dfsg-1_armhf.deb
217a7030a774dabd89fc322dda795e6b 3187568 debug optional hyphy-pt-dbgsym_2.5.69+dfsg-1_armhf.deb
d96ee600339a581ef882706cbaf7ca15 769512 science optional hyphy-pt_2.5.69+dfsg-1_armhf.deb
6511400eebba7dc51507b32ac1158af1 9057 science optional hyphy_2.5.69+dfsg-1_armhf.buildinfo
Thu Mar 6 10:04:52 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-armhf_3-14085.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tX5jPBTX/hyphy_2.5.69+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tX5jPBTX/hyphy_2.5.69+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tX5jPBTX/hyphy_2.5.69+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tX5jPBTX/b1/hyphy_2.5.69+dfsg-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.tX5jPBTX/b2/hyphy_2.5.69+dfsg-1_armhf.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.004s)
0.004s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 234ms
CPU time consumed: 235ms
Thu Mar 6 10:04:52 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Thu Mar 6 10:04:52 UTC 2025 I: hyphy from unstable built successfully and reproducibly on armhf.
Thu Mar 6 10:04:53 UTC 2025 I: Submitting .buildinfo files to external archives:
Thu Mar 6 10:04:53 UTC 2025 I: Submitting 12K b1/hyphy_2.5.69+dfsg-1_armhf.buildinfo.asc
Thu Mar 6 10:04:55 UTC 2025 I: Submitting 12K b2/hyphy_2.5.69+dfsg-1_armhf.buildinfo.asc
Thu Mar 6 10:04:56 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Mar 6 10:04:56 UTC 2025 I: Done submitting .buildinfo files.
Thu Mar 6 10:04:56 UTC 2025 I: Removing signed hyphy_2.5.69+dfsg-1_armhf.buildinfo.asc files:
removed './b1/hyphy_2.5.69+dfsg-1_armhf.buildinfo.asc'
removed './b2/hyphy_2.5.69+dfsg-1_armhf.buildinfo.asc'