Sun Nov 10 07:16:14 UTC 2024 I: starting to build hyphy/unstable/i386 on jenkins on '2024-11-10 07:15' Sun Nov 10 07:16:14 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_17/26643/console.log Sun Nov 10 07:16:14 UTC 2024 I: Downloading source for unstable/hyphy=2.5.63+dfsg-1 --2024-11-10 07:16:15-- http://deb.debian.org/debian/pool/main/h/hyphy/hyphy_2.5.63%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2420 (2.4K) [text/prs.lines.tag] Saving to: ‘hyphy_2.5.63+dfsg-1.dsc’ 0K .. 100% 248M=0s 2024-11-10 07:16:15 (248 MB/s) - ‘hyphy_2.5.63+dfsg-1.dsc’ saved [2420/2420] Sun Nov 10 07:16:15 UTC 2024 I: hyphy_2.5.63+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: 2.5.63+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier , Nilesh Patra Homepage: https://hyphy.org/ Standards-Version: 4.7.0 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: ca9c51d52fadd9e6aafecb9ec2480fb2011d5cd7 2626580 hyphy_2.5.63+dfsg.orig.tar.xz 71ed09e78052f951006d9738c9ebe1ee7ca0f182 17244 hyphy_2.5.63+dfsg-1.debian.tar.xz Checksums-Sha256: 44a4f7c83eb8854454c42a4e6c48b640ab2e1d93b88f55f7e38a34cf6701aa64 2626580 hyphy_2.5.63+dfsg.orig.tar.xz 05a83c4172d4acef5e9154783c0b5faed04c0f3a8849d223c5efb6640d70cdae 17244 hyphy_2.5.63+dfsg-1.debian.tar.xz Files: b126e5e1a1ec2212eb3986a2bf4d03e1 2626580 hyphy_2.5.63+dfsg.orig.tar.xz 390b7033ba1bff678009b433f4f36006 17244 hyphy_2.5.63+dfsg-1.debian.tar.xz Dgit: 1e16be5ba4764d2080f73aa823309fc90e8fd57c debian archive/debian/2.5.63+dfsg-1 https://git.dgit.debian.org/hyphy -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcnamMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrxgA//a90YE+StFHEo5b7boviZ9qdrHHmC 8ERoXCSiYD9zdAXVQZFRmUNyZ3j58Avt1yG08+9NjsEjVkZgPwIwXD9LwfyfaOHf v8JTQlHYIeithR8/rlPooxepx5luPEUKsBRuK0KV9meXTaQ4uUc38CJeA/Cmv2nq hdEXNZOX1UkmAfdZaj9O5J+t0o0E2RQrhqe2SlRa0snA8iY+L+akzwl5lU4qlAsc P1xFmk7IoaQjFSbVMvq4ZtDEbHyNPpZrGdmfAMOjddBbXNymS6UegbjC6xRGizTr 70LwhjfxKCSgYWbvJYH9x1tbOJaCpGNPf1PlHM6J34H/Nq03eNZxaL6IYso4HlCZ Lba+0EGn1K9VO/9Z8UvTPhde3f328WKVaqdFF6miSvN7/SDtRv+koDndRmx2P1X+ WrToyBoH8yjoXRqdN1AOUOWnyjNlF9GQ9/eZ46ONUiWvLCw7GKjh6BDsf+SYsEif 2Ebtce++lOM25umTZ0e/aGV0SO9yHmlCnjVvT9ls3h4nzhNypUoIUlUUhu0GVwgQ D6M4E8QUWlYMuZ3EAmXDyVtD3iPtmj2mT5wOvjr7WvyzC7N24uFnQQaEy+eY4t9M F3cuDtEiRIFISoMu7XwoT9vrwbxjhvo/JLATb7249C14ILthIK9cffCaY5iduHtK MTMwk3uqddQQwgs= =hOV1 -----END PGP SIGNATURE----- Sun Nov 10 07:16:15 UTC 2024 I: Checking whether the package is not for us Sun Nov 10 07:16:15 UTC 2024 I: Starting 1st build on remote node infom07-i386.debian.net. Sun Nov 10 07:16:15 UTC 2024 I: Preparing to do remote build '1' on infom07-i386.debian.net. Sun Nov 10 07:20:46 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 9 19:16:19 -12 2024 I: pbuilder-time-stamp: 1731222979 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: using eatmydata during job I: Copying source file I: copying [hyphy_2.5.63+dfsg-1.dsc] I: copying [./hyphy_2.5.63+dfsg.orig.tar.xz] I: copying [./hyphy_2.5.63+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 3 12:19:47 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hyphy_2.5.63+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting hyphy in hyphy-2.5.63+dfsg dpkg-source: info: unpacking hyphy_2.5.63+dfsg.orig.tar.xz dpkg-source: info: unpacking hyphy_2.5.63+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/3771/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='cd0a7e57e41644348373144af61f686e' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='3771' 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.gVX3DHpc/pbuilderrc_bgbO --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.gVX3DHpc/b1 --logfile b1/build.log hyphy_2.5.63+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom07-i386 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3771/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, mpi-default-dev, libcurl4-gnutls-dev | libcurl4-dev, libssl-dev, libsqlite3-dev, pkgconf, libpython3-all-dev, python3-all-dev:any, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 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-i686-linux-gnu{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} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhwloc-dev{a} libhwloc15{a} libicu72{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-2.5-0{a} libldap-dev{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} libnsl2{a} libnuma-dev{a} libnuma1{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libslurm41t64{a} libsqlite3-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{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} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 136 newly installed, 0 to remove and 0 not upgraded. Need to get 88.8 MB of archives. After unpacking 321 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.7-3 [814 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.7-3 [2236 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.7-3 [1964 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-10 [102 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 chrpath i386 0.18-1 [14.0 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.1 [733 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b5 [298 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libjsoncpp26 i386 1.9.6-2 [90.0 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 58 http://deb.debian.org/debian unstable/main i386 comerr-dev i386 2.1-1.47.1-1+b1 [55.3 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 65 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libgfortran-14-dev i386 14.2.0-8 [800 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 gfortran-14-i686-linux-gnu i386 14.2.0-8 [12.5 MB] Get: 74 http://deb.debian.org/debian unstable/main i386 gfortran-14 i386 14.2.0-8 [12.2 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libhwloc15 i386 2.11.2-1 [177 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 hwloc-nox i386 2.11.2-1 [229 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libgssrpc4t64 i386 1.21.3-3 [63.1 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libkadm5clnt-mit12 i386 1.21.3-3 [43.2 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libkdb5-10t64 i386 1.21.3-3 [45.1 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libkadm5srv-mit12 i386 1.21.3-3 [57.0 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 krb5-multidev i386 1.21.3-3 [126 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libbrotli-dev i386 1.1.0-2+b5 [313 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.4.0-1+b1 [74.9 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.6.0-1 [154 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.6.0-1 [20.2 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.0-1 [403 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libunbound8 i386 1.22.0-1 [632 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libgnutls-dane0t64 i386 3.8.6-2+b1 [440 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libgnutls-openssl27t64 i386 3.8.6-2+b1 [440 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libp11-kit-dev i386 0.25.5-2+b1 [208 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-2+b2 [330 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libgmp-dev i386 2:6.3.0+dfsg-2+b2 [661 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libgnutls28-dev i386 3.8.6-2+b1 [1449 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libkrb5-dev i386 1.21.3-3 [15.7 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libldap-dev i386 2.5.18+dfsg-3+b1 [324 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libnghttp3-dev i386 1.4.0-1+b1 [99.9 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls-dev i386 1.6.0-1 [24.7 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libngtcp2-dev i386 1.6.0-1 [206 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libssl-dev i386 3.3.2-2 [2790 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libcurl4-gnutls-dev i386 8.11.0-1 [533 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.4-1 [165 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libnuma1 i386 2.0.18-1+b1 [23.9 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libnuma-dev i386 2.0.18-1+b1 [38.8 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.4.7-8 [395 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libltdl-dev i386 2.4.7-8 [167 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libhwloc-dev i386 2.11.2-1 [271 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libmpich12 i386 4.2.0-14 [1518 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libslurm41t64 i386 24.05.4-1 [739 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 mpich i386 4.2.0-14 [235 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libmpich-dev i386 4.2.0-14 [2494 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.7-3 [2170 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.7-3 [5282 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.12.6-1 [9956 B] Get: 130 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.12.6-1 [1068 B] Get: 131 http://deb.debian.org/debian unstable/main i386 libsqlite3-dev i386 3.46.1-1 [1193 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 mpi-default-dev i386 1.17 [3144 B] Get: 133 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.12.6-1 [1040 B] Get: 134 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.7-3 [505 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.12.6-1 [26.1 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.12.6-1 [1068 B] Fetched 88.8 MB in 1s (86.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19956 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.7-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_i386.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:i386 (3.12.7-3) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20276 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_i386.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21338 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_i386.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:i386. 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Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.2-10_i386.deb ... Unpacking bsdextrautils (2.40.2-10) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../011-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. 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Selecting previously unselected package libxml2:i386. Preparing to unpack .../021-libxml2_2.12.7+dfsg+really2.9.14-0.1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package libarchive13t64:i386. Preparing to unpack .../022-libarchive13t64_3.7.4-1.1_i386.deb ... Unpacking libarchive13t64:i386 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../023-libbrotli1_1.1.0-2+b5_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b5) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../024-libsasl2-modules-db_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../025-libsasl2-2_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../026-libldap-2.5-0_2.5.18+dfsg-3+b1_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../027-libnghttp2-14_1.64.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:i386. Preparing to unpack .../028-libpsl5t64_0.21.2-1.1+b1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../029-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:i386. Preparing to unpack .../030-libssh2-1t64_1.11.1-1_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:i386. Preparing to unpack .../031-libcurl4t64_8.11.0-1_i386.deb ... Unpacking libcurl4t64:i386 (8.11.0-1) ... Selecting previously unselected package libjsoncpp26:i386. Preparing to unpack .../032-libjsoncpp26_1.9.6-2_i386.deb ... Unpacking libjsoncpp26:i386 (1.9.6-2) ... Selecting previously unselected package librhash1:i386. Preparing to unpack .../033-librhash1_1.4.5-1_i386.deb ... Unpacking librhash1:i386 (1.4.5-1) ... Selecting previously unselected package libuv1t64:i386. Preparing to unpack .../034-libuv1t64_1.48.0-7_i386.deb ... Unpacking libuv1t64:i386 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../035-cmake_3.30.5-1_i386.deb ... Unpacking cmake (3.30.5-1) ... Selecting previously unselected package comerr-dev:i386. Preparing to unpack .../036-comerr-dev_2.1-1.47.1-1+b1_i386.deb ... Unpacking comerr-dev:i386 (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../037-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. 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Setting up libbrotli1:i386 (1.1.0-2+b5) ... Setting up libuv1t64:i386 (1.48.0-7) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:i386 (2.1.12-stable-10+b1) ... Setting up libcom-err2:i386 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libpsl-dev:i386 (0.21.2-1.1+b1) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Nov 10 07:17:32 UTC 2024. Universal Time is now: Sun Nov 10 07:17:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libunbound8:i386 (1.22.0-1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-2+b2) ... Setting up libexpat1-dev:i386 (2.6.4-1) ... Setting up libgnutls-dane0t64:i386 (3.8.6-2+b1) ... Setting up libsqlite3-dev:i386 (3.46.1-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:i386 (1.9.6-2) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up comerr-dev:i386 (2.1-1.47.1-1+b1) ... Setting up libssl-dev:i386 (3.3.2-2) ... Setting up libhwloc15:i386 (2.11.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libltdl7:i386 (2.4.7-8) ... Setting up libidn2-dev:i386 (2.3.7-2+b1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up libgfortran5:i386 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:i386 (1.4.0-1+b1) ... Setting up libnghttp3-dev:i386 (1.4.0-1+b1) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:i386 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libmpich12:i386 (4.2.0-14) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libslurm41t64 (24.05.4-1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:i386 (1.6.0-1) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:i386 (1.4.5-1) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtasn1-6-dev:i386 (4.19.0-3+b3) ... Setting up readline-common (8.2-5) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libbrotli-dev:i386 (1.1.0-2+b5) ... Setting up chrpath (0.18-1) ... Setting up libngtcp2-crypto-gnutls8:i386 (1.6.0-1) ... Setting up libp11-kit-dev:i386 (0.25.5-2+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:i386 (14.2.0-8) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:i386 (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:i386 (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up hwloc-nox (2.11.2-1) ... Setting up libngtcp2-crypto-gnutls-dev:i386 (1.6.0-1) ... Setting up libngtcp2-dev:i386 (1.6.0-1) ... Setting up libldap-2.5-0:i386 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:i386 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:i386 (2.0.18-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:i386 (2.4.7-8) ... Setting up libldap-dev:i386 (2.5.18+dfsg-3+b1) ... Setting up gfortran-14-i686-linux-gnu (14.2.0-8) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libssh2-1-dev:i386 (1.11.1-1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libhwloc-dev:i386 (2.11.2-1) ... Setting up gfortran-14 (14.2.0-8) ... Setting up libarchive13t64:i386 (3.7.4-1.1) ... Setting up libgnutls28-dev:i386 (3.8.6-2+b1) ... Setting up libnghttp2-dev:i386 (1.64.0-1) ... Setting up libcurl4t64:i386 (8.11.0-1) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Setting up mpich (4.2.0-14) ... 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 libcurl3t64-gnutls:i386 (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:i386 (1.21.3-3) ... Setting up librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libmpich-dev:i386 (4.2.0-14) ... update-alternatives: using /usr/include/i386-linux-gnu/mpich to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up mpi-default-dev (1.17) ... Setting up libnsl2:i386 (1.3.0-3+b3) ... Setting up cmake (3.30.5-1) ... Setting up libkadm5clnt-mit12:i386 (1.21.3-3) ... Setting up libpython3.12-stdlib:i386 (3.12.7-3) ... Setting up libkdb5-10t64:i386 (1.21.3-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:i386 (3.12.7-3) ... Setting up libkadm5srv-mit12:i386 (1.21.3-3) ... Setting up libpython3-stdlib:i386 (3.12.6-1) ... Setting up krb5-multidev:i386 (1.21.3-3) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:i386 (3.12.7-3) ... Setting up libkrb5-dev:i386 (1.21.3-3) ... Setting up python3.12-dev (3.12.7-3) ... Setting up libpython3-dev:i386 (3.12.6-1) ... Setting up python3-all (3.12.6-1) ... Setting up libcurl4-gnutls-dev:i386 (8.11.0-1) ... Setting up libpython3-all-dev:i386 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-all-dev (3.12.6-1) ... Processing triggers for libc-bin (2.40-3) ... 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-2.5.63+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_2.5.63+dfsg-1_source.changes dpkg-buildpackage: info: source package hyphy dpkg-buildpackage: info: source version 2.5.63+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg' dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+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-2.5.63+dfsg' dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_SSE4_EXTENSIONS -- Performing Test HAVE_SSE4_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set compiler flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 Set linker flags to -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -- Could NOT find BLAS (missing: BLAS_LIBRARIES) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found CURL: /usr/lib/i386-linux-gnu/libcurl.so (found version "8.11.0") /usr/lib/i386-linux-gnu/libcurl.so Node not installed; API documentation will not be generated -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Checking for module 'sqlite3' -- Found sqlite3, version 3.46.1 -- Found SQLITE3: /usr/lib/i386-linux-gnu/libsqlite3.so -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found suitable version "1.3.1", minimum required is "1.2.9") /usr/share/hyphy -- Found MPI_C: /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so (found version "4.1") -- Found MPI_CXX: /usr/lib/i386-linux-gnu/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 -msse4.1 -fopenmp -- Configuring done (9.2s) -- 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-2.5.63+dfsg/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg' dh_auto_build -- MP MPI cd obj-i686-linux-gnu && make -j6 "INSTALL=install --strip-program=true" MP MPI VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.63+dfsg -B/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 MP make[3]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.63+dfsg -B/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MP.dir/all make[4]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/depend make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.63+dfsg /build/reproducible-path/hyphy-2.5.63+dfsg /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu/CMakeFiles/hyphy.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/hyphy.dir/build.make CMakeFiles/hyphy.dir/build make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/_hyExecutionContext.cpp [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/associative_list.cpp /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/alignment.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllistx_iterator.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllistxl.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast 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-Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/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-2.5.63+dfsg/src/core/baseobj.cpp [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlan.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlanhelpers.cpp [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -MF CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -MF CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/category.cpp.o -MF CMakeFiles/hyphy.dir/src/core/category.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/category.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/category.cpp [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/constant.cpp.o -MF CMakeFiles/hyphy.dir/src/core/constant.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/constant.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/dataset_filter_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-2.5.63+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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/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-2.5.63+dfsg/src/core/fisher_exact.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula.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-2.5.63+dfsg/src/core/formula.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/formula_parsing_context.cpp [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -MF CMakeFiles/hyphy.dir/src/core/fstring.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD 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-D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -MF CMakeFiles/hyphy.dir/src/core/global_things.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/global_things.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/hyFile.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/list.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -MF CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o -MF CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/matrix_mult.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -MF CMakeFiles/hyphy.dir/src/core/nexus.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/ntuplestorage.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/operation.cpp.o -MF CMakeFiles/hyphy.dir/src/core/operation.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/operation.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -MF CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/site.cpp.o -MF CMakeFiles/hyphy.dir/src/core/site.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/stack.cpp.o -MF CMakeFiles/hyphy.dir/src/core/stack.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/stack.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/stack.cpp [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/strings.cpp.o -MF CMakeFiles/hyphy.dir/src/core/strings.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/strings.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/strings.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -MF CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/time_difference.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/topology.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/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-2.5.63+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -MF CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/translation_table.cpp [ 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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree.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-2.5.63+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/trie.cpp.o -MF CMakeFiles/hyphy.dir/src/core/trie.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/trie.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variable.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variable.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variable.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/variablecontainer.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/vector.cpp.o -MF CMakeFiles/hyphy.dir/src/core/vector.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/vector.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bayesgraph.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bayesgraph2.cpp [ 85%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -MF CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -MF CMakeFiles/hyphy.dir/src/new/scfg.cpp.o.d -o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/utils/hyphyunixutils.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib/mersenne_twister.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -MF CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o.d -o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/hyphy.dir/src/mains/unix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -MF CMakeFiles/hyphy.dir/src/mains/unix.cpp.o.d -o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/mains/unix.cpp [100%] Linking CXX executable hyphy /usr/bin/cmake -E cmake_link_script CMakeFiles/hyphy.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o CMakeFiles/hyphy.dir/src/core/avllist.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o CMakeFiles/hyphy.dir/src/core/category.cpp.o CMakeFiles/hyphy.dir/src/core/constant.cpp.o CMakeFiles/hyphy.dir/src/core/dataset.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o CMakeFiles/hyphy.dir/src/core/formula.cpp.o CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o CMakeFiles/hyphy.dir/src/core/fstring.cpp.o CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o CMakeFiles/hyphy.dir/src/core/global_things.cpp.o CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o CMakeFiles/hyphy.dir/src/core/hyFile.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o CMakeFiles/hyphy.dir/src/core/list.cpp.o CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o CMakeFiles/hyphy.dir/src/core/matrix.cpp.o CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o CMakeFiles/hyphy.dir/src/core/nexus.cpp.o CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o CMakeFiles/hyphy.dir/src/core/operation.cpp.o CMakeFiles/hyphy.dir/src/core/parser.cpp.o CMakeFiles/hyphy.dir/src/core/parser2.cpp.o CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o CMakeFiles/hyphy.dir/src/core/site.cpp.o CMakeFiles/hyphy.dir/src/core/stack.cpp.o CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/hyphy.dir/src/core/strings.cpp.o CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o CMakeFiles/hyphy.dir/src/core/topology.cpp.o CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o CMakeFiles/hyphy.dir/src/core/tree.cpp.o CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/trie.cpp.o CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o CMakeFiles/hyphy.dir/src/core/variable.cpp.o CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o CMakeFiles/hyphy.dir/src/core/vector.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o CMakeFiles/hyphy.dir/src/new/bgm.cpp.o CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o CMakeFiles/hyphy.dir/src/new/scfg.cpp.o CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o CMakeFiles/hyphy.dir/src/mains/unix.cpp.o -o hyphy -ldl -lpthread 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CMakeFiles/MP.dir/build.make CMakeFiles/MP.dir/build make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/MP.dir/build'. make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' [100%] Built target MP make[4]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/Makefile2 MPI make[3]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.63+dfsg -B/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu/CMakeFiles 20 make -f CMakeFiles/Makefile2 CMakeFiles/MPI.dir/all make[4]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/depend make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.63+dfsg /build/reproducible-path/hyphy-2.5.63+dfsg /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu/CMakeFiles/HYPHYMPI.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/HYPHYMPI.dir/build.make CMakeFiles/HYPHYMPI.dir/build make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/_hyExecutionContext.cpp [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/alignment.cpp [ 0%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/associative_list.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllist.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllistx.cpp [ 5%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllistx_iterator.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllistxl.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/avllistxl_iterator.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/baseobj.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/baseobj.cpp [ 10%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlan.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlan2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlan2.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanhelpers.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlanhelpers.cpp [ 15%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/batchlanruntime.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/batchlanruntime.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/calcnode.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/calcnode.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/category.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/category.cpp [ 20%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/constant.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/constant.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/dataset.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/dataset_filter.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/dataset_filter_numeric.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/dataset_filter_numeric.cpp [ 25%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fisher_exact.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/fisher_exact.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/formula.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/formula_parsing_context.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/formula_parsing_context.cpp [ 30%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/fstring.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/fstring.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_object_lists.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/global_object_lists.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/global_things.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/global_things.cpp [ 35%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hbl_env.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/hbl_env.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/hyFile.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/likefunc.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/likefunc2.cpp [ 40%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/likefuncocl.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/list.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/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-2.5.63+dfsg/src/core/mathobj.cpp [ 45%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/matrix.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/matrix_mult.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/nexus.cpp [ 50%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/ntuplestorage.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/operation.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/parser.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/parser2.cpp [ 55%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/polynoml.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/simplelist.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/site.cpp [ 60%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/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-2.5.63+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_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_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-2.5.63+dfsg/src/core/string_buffer.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/string_file_wrapper.cpp [ 65%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/strings.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/time_difference.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/topology.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/translation_table.cpp [ 70%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/tree.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/tree_evaluator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/tree_iterator.cpp [ 75%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/trie.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/trie_iterator.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/variable.cpp [ 80%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/variablecontainer.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -w -Weffc++ -Wextra -Wall -Wno-int-to-pointer-cast -MD -MT CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/core/vector.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bayesgraph.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bayesgraph2.cpp [ 85%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bgm.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/bgm2.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -Weffc++ -Wextra -Wall -MD -MT CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/new/scfg.cpp [ 90%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o -c 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-MD -MT CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib/regex.cpp [ 95%] Building CXX object CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__HYPHYMPI__ -D__UNIX__ -D__ZLIB__ -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/core/include -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/contrib -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/lib/Link -I/build/reproducible-path/hyphy-2.5.63+dfsg/src/new/include -I/usr/lib/i386-linux-gnu/mpich/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 -w -Weffc++ -Wextra -Wall -fopenmp -MD -MT CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -MF CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o.d -o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -c /build/reproducible-path/hyphy-2.5.63+dfsg/src/mains/unix.cpp [100%] Linking CXX executable HYPHYMPI /usr/bin/cmake -E cmake_link_script CMakeFiles/HYPHYMPI.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hyphy-2.5.63+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14 -msse4.1 CMakeFiles/HYPHYMPI.dir/src/core/_hyExecutionContext.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/alignment.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/associative_list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistx_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/avllistxl.cpp.o 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CMakeFiles/HYPHYMPI.dir/src/core/hyFile.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefunc2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/likefuncocl.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/list.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/mathobj.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/matrix.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/matrix_mult.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/nexus.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/ntuplestorage.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/operation.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/polynoml.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/simplelist.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/site.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/stack.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_buffer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/string_file_wrapper.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/strings.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/time_difference.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/topology.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/translation_table.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_evaluator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/tree_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/trie_iterator.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variable.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/variablecontainer.cpp.o CMakeFiles/HYPHYMPI.dir/src/core/vector.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bayesgraph2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/bgm2.cpp.o CMakeFiles/HYPHYMPI.dir/src/new/scfg.cpp.o CMakeFiles/HYPHYMPI.dir/src/utils/hyphyunixutils.cpp.o CMakeFiles/HYPHYMPI.dir/src/contrib/mersenne_twister.cpp.o CMakeFiles/HYPHYMPI.dir/src/contrib/regex.cpp.o CMakeFiles/HYPHYMPI.dir/src/mains/unix.cpp.o -o HYPHYMPI -Wl,-rpath,/usr/lib/i386-linux-gnu/mpich/lib: -ldl -lpthread -lcrypto -lcurl -lssl -lsqlite3 /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/mpich/lib/libmpichcxx.so /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so /usr/lib/gcc/i686-linux-gnu/14/libgomp.so /usr/lib/i386-linux-gnu/libpthread.a make[5]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' [100%] Built target HYPHYMPI make -f CMakeFiles/MPI.dir/build.make CMakeFiles/MPI.dir/depend make[5]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hyphy-2.5.63+dfsg /build/reproducible-path/hyphy-2.5.63+dfsg /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu /build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu 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./tests/hbltests/UnitTests/HBLCommands/HarvestFrequencies.bf ./tests/hbltests/UnitTests/HBLCommands/IBeta.bf ./tests/hbltests/UnitTests/HBLCommands/IGamma.bf ./tests/hbltests/UnitTests/HBLCommands/If.bf ./tests/hbltests/UnitTests/HBLCommands/Integrate.bf ./tests/hbltests/UnitTests/HBLCommands/Inverse.bf ./tests/hbltests/UnitTests/HBLCommands/JSON.bf ./tests/hbltests/UnitTests/HBLCommands/Join.bf ./tests/hbltests/UnitTests/HBLCommands/LUDecompose.bf ./tests/hbltests/UnitTests/HBLCommands/LUSolve.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthan.bf ./tests/hbltests/UnitTests/HBLCommands/Lessthanorequalto.bf ./tests/hbltests/UnitTests/HBLCommands/LnGamma.bf ./tests/hbltests/UnitTests/HBLCommands/LoadFunctionLibrary.bf ./tests/hbltests/UnitTests/HBLCommands/Log.bf ./tests/hbltests/UnitTests/HBLCommands/MAccess_bracket.bf ./tests/hbltests/UnitTests/HBLCommands/Max.bf ./tests/hbltests/UnitTests/HBLCommands/Min.bf ./tests/hbltests/UnitTests/HBLCommands/Model.bf ./tests/hbltests/UnitTests/HBLCommands/Percentsign.bf ./tests/hbltests/UnitTests/HBLCommands/Random.bf ./tests/hbltests/UnitTests/HBLCommands/ReplicateConstraint.bf ./tests/hbltests/UnitTests/HBLCommands/RequireVersion.bf ./tests/hbltests/UnitTests/HBLCommands/RerootTree.bf ./tests/hbltests/UnitTests/HBLCommands/Return.bf ./tests/hbltests/UnitTests/HBLCommands/Rows.bf ./tests/hbltests/UnitTests/HBLCommands/Simplex.bf ./tests/hbltests/UnitTests/HBLCommands/Simplify.bf ./tests/hbltests/UnitTests/HBLCommands/SimulateDataSet.bf ./tests/hbltests/UnitTests/HBLCommands/Sin.bf ./tests/hbltests/UnitTests/HBLCommands/Sqrt.bf ./tests/hbltests/UnitTests/HBLCommands/Sscanf.bf ./tests/hbltests/UnitTests/HBLCommands/Subtract.bf ./tests/hbltests/UnitTests/HBLCommands/Tan.bf ./tests/hbltests/UnitTests/HBLCommands/Time.bf ./tests/hbltests/UnitTests/HBLCommands/TipCount.bf ./tests/hbltests/UnitTests/HBLCommands/TipName.bf ./tests/hbltests/UnitTests/HBLCommands/Topology.bf ./tests/hbltests/UnitTests/HBLCommands/Transpose.bf ./tests/hbltests/UnitTests/HBLCommands/Tree.bf ./tests/hbltests/UnitTests/HBLCommands/Type.bf ./tests/hbltests/UnitTests/HBLCommands/While.bf ./tests/hbltests/UnitTests/HBLCommands/ZCDF.bf ./tests/hbltests/UnitTests/HBLCommands/assert.bf ./tests/hbltests/UnitTests/HBLCommands/break.bf ./tests/hbltests/UnitTests/HBLCommands/fscanf_fprintf.bf ./tests/hbltests/UnitTests/HBLCommands/include.bf ./tests/hbltests/UnitTests/HBLCommands/lfunction.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_iofunctions.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_math.bf ./tests/hbltests/UnitTests/HBLCommands/libv3_utilityfunctions.bf ./tests/hbltests/UnitTests/HBLCommands/namespace.bf \n\n------------------------ALL TEST PASSED------------------------------------\n make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j6 install DESTDIR=/build/reproducible-path/hyphy-2.5.63\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hyphy-2.5.63+dfsg -B/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Binary/F81.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/F81.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Nucleotide/REV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/K2P -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/User/Nucleotide/JC69 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Estimated -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/AAEFV/Equal -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Estimated -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/NucEFV/Equal -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/aa.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/codon.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/dinuc.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params. -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Equal -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/SubstitutionClasses/nuc.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/chooseDistanceFormula.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/molclockBootstrap.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SeqAlignShared.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LocalMolClock.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GateauxMR.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ModelTest.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BGM.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_CMS_Aux.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper3.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestBranchDNDS.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_MFReader_.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/F_ST.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/doSPRSwap.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/RelativeRatio.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TopologySearch.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LRTRecombTest.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonToProtein.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MolecularClock.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/selectModelParameters.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GARD.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/LEISR.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGASimProcessor.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MGvsGY.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-joint-fitter.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/globalChecker.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GUI -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GUI/crayolaColors.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Gateaux.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/bayesgraph.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf -- Installing: 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-- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/CodonModelCompare.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ClusterAnalysis.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf -- Installing: 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/build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/NJ.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/DBTools.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/GrabBag.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/PostScript.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/MPITools.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-selector.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/doNNISwap.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/KHTest.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/simpleBootstrap.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/files.lst -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SandNSAmbigs.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TestCladeMeans.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TreeTools.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.dat -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16A -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/S4 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAF81 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/190 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/PCH -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Default -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MolClockAllRoots.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SequentialAddition.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/queryTree.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/GA_CHC.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSequences.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper1.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AddABias.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/partitionSequences.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MergeSites.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SGEmulator_MF.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN84 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_aa -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/T3P -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_RV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P_RV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/PC_MH -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/K2P -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/JC69 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_binary -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/p_Distance_codon -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93_RV -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/TN93 -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/FitnessAAModels.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_tipDater.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/error-filter.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/MSS-selector-2.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/qndhelper2.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/relrateBootstrap.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/ConvertDataFile.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/UpperBound.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/_BMS_Aux.ibf -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Vertebratemtdna.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Euplotid_Nuclear.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Flatworm_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Yeast_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ascidian_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Mold_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/GeneticCodes/Ciliate.cod -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/data -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/data/brown.nuc -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/data/p51.aa -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/data/integrase_BDA.nex -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/data/p51.nex -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/bin/hyphy -- Installing: /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/bin/HYPHYMPI -- Set non-toolchain portion of runtime path of "/build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/bin/HYPHYMPI" to "" make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg' # convert a few ISO-8859-1 files to address national-encoding set -e \ ; for file in /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf /build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl /build/reproducible-path/hyphy-2.5.63+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-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf.new' -> '/build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/PARRIS.bf' renamed '/build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl.new' -> '/build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl' renamed '/build/reproducible-path/hyphy-2.5.63+dfsg/debian/tmp/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst.new' -> '/build/reproducible-path/hyphy-2.5.63+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-2.5.63+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg' dh_install -i make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg' debian/rules override_dh_installdocs-arch make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.63+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-2.5.63+dfsg' debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/reproducible-path/hyphy-2.5.63+dfsg' dh_installdocs -i make[1]: Leaving directory '/build/reproducible-path/hyphy-2.5.63+dfsg' dh_installchangelogs -O--buildsystem=cmake dh_installexamples -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'hyphy-mpi-dbgsym' in '../hyphy-mpi-dbgsym_2.5.63+dfsg-1_i386.deb'. dpkg-deb: building package 'hyphy-pt-dbgsym' in '../hyphy-pt-dbgsym_2.5.63+dfsg-1_i386.deb'. dpkg-deb: building package 'hyphy-mpi' in '../hyphy-mpi_2.5.63+dfsg-1_i386.deb'. dpkg-deb: building package 'hyphy-pt' in '../hyphy-pt_2.5.63+dfsg-1_i386.deb'. dpkg-deb: building package 'hyphy-common' in '../hyphy-common_2.5.63+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../hyphy_2.5.63+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../hyphy_2.5.63+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/3771 and its subdirectories I: Current time: Sat Nov 9 19:20:45 -12 2024 I: pbuilder-time-stamp: 1731223245 Sun Nov 10 07:20:47 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom08-i386.debian.net. Sun Nov 10 07:20:47 UTC 2024 I: Preparing to do remote build '2' on infom08-i386.debian.net. Sun Nov 10 07:22:30 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. Sun Nov 10 07:22:31 UTC 2024 I: hyphy_2.5.63+dfsg-1_i386.changes: Format: 1.8 Date: Sun, 03 Nov 2024 11:54:22 +0100 Source: hyphy Binary: hyphy-common hyphy-mpi hyphy-mpi-dbgsym hyphy-pt hyphy-pt-dbgsym Architecture: all i386 Version: 2.5.63+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier 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 (2.5.63+dfsg-1) unstable; urgency=medium . * New upstream version 2.5.63+dfsg * set-zlib-after-setting-default-libs.patch: unfuzz. * use_debian_sqlite.patch: unfuzz. * d/rules: locate all HYPHYMPI to erase DT_RUNPATH. Checksums-Sha1: 78924819119e969f82ae3765ec82900d0929ac6c 606328 hyphy-common_2.5.63+dfsg-1_all.deb e24b4babec7a61d6b2d911cc336087e0f88cda84 3172796 hyphy-mpi-dbgsym_2.5.63+dfsg-1_i386.deb 5b4169a35a4be7f5444142b9bc7d7f8eeaf2825c 1040300 hyphy-mpi_2.5.63+dfsg-1_i386.deb 5ffd1309beb6aa0083a0daf7cf896e9704b68f52 3109692 hyphy-pt-dbgsym_2.5.63+dfsg-1_i386.deb 227cf25a0965220f9e57ceb8473ae0a2ae976b9b 1018904 hyphy-pt_2.5.63+dfsg-1_i386.deb 87d42876478bc85c5cc4eb6b63d25b658a14d269 9370 hyphy_2.5.63+dfsg-1_i386.buildinfo Checksums-Sha256: 3b7aa5d312a64bfddd7885ff38d36dc9c3ca3af514706ecf2120a18770195dea 606328 hyphy-common_2.5.63+dfsg-1_all.deb 74207029278d701d303d1f32bcd62aff94b91fc068a8a76389736ec821e2ce1f 3172796 hyphy-mpi-dbgsym_2.5.63+dfsg-1_i386.deb f7ab658aba7002ab1d9bf0f55db38fc33a8ca8011ac8c8036b387dfb0db3bbaa 1040300 hyphy-mpi_2.5.63+dfsg-1_i386.deb 85b15ecf32235273e76b9ce023bd141bde17cc9688aa420854755398bfa01c1f 3109692 hyphy-pt-dbgsym_2.5.63+dfsg-1_i386.deb 2e8f49f61e95367d315fb191cd2db65fe9b5ccb61d13ab9831f65249c256c155 1018904 hyphy-pt_2.5.63+dfsg-1_i386.deb 03e4d35cee3e8723c41562480425a3cfbc1a45b03a106389aea0746f60b2c660 9370 hyphy_2.5.63+dfsg-1_i386.buildinfo Files: 1ff56b5ebe9079ae65cdf68df56fd063 606328 science optional hyphy-common_2.5.63+dfsg-1_all.deb 557352b6f5d68e91d9746adcce208187 3172796 debug optional hyphy-mpi-dbgsym_2.5.63+dfsg-1_i386.deb be9f9746936eb86b1b69e42690d219cb 1040300 science optional hyphy-mpi_2.5.63+dfsg-1_i386.deb d545b4186c506acc066e04b623de39e1 3109692 debug optional hyphy-pt-dbgsym_2.5.63+dfsg-1_i386.deb bac207e20781529a31d42571b3bf1ce8 1018904 science optional hyphy-pt_2.5.63+dfsg-1_i386.deb f167f06b38450e7002a3e625be705290 9370 science optional hyphy_2.5.63+dfsg-1_i386.buildinfo Sun Nov 10 07:22:32 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_17-26643.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.gVX3DHpc/hyphy_2.5.63+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.gVX3DHpc/hyphy_2.5.63+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.gVX3DHpc/hyphy_2.5.63+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.gVX3DHpc/b1/hyphy_2.5.63+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.gVX3DHpc/b2/hyphy_2.5.63+dfsg-1_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.586s) 0.586s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.133s) 0.133s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 978ms CPU time consumed: 978ms Sun Nov 10 07:22:34 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sun Nov 10 07:22:34 UTC 2024 I: hyphy from unstable built successfully and reproducibly on i386. Sun Nov 10 07:22:35 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Nov 10 07:22:35 UTC 2024 I: Submitting 12K b1/hyphy_2.5.63+dfsg-1_i386.buildinfo.asc Sun Nov 10 07:22:36 UTC 2024 I: Submitting 12K b2/hyphy_2.5.63+dfsg-1_i386.buildinfo.asc Sun Nov 10 07:22:37 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Nov 10 07:22:37 UTC 2024 I: Done submitting .buildinfo files. Sun Nov 10 07:22:37 UTC 2024 I: Removing signed hyphy_2.5.63+dfsg-1_i386.buildinfo.asc files: removed './b1/hyphy_2.5.63+dfsg-1_i386.buildinfo.asc' removed './b2/hyphy_2.5.63+dfsg-1_i386.buildinfo.asc'