Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bali-phy/bali-phy_3.6.0+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bali-phy-3.6.0+dfsg-1jjjkfzxo/bali-phy_3.6.0+dfsg-1_amd64.buildinfo Get source package info: bali-phy=3.6.0+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/bali-phy/3.6.0+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-6 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.3 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210201-1 file=1:5.39-3 findutils=4.8.0-1 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblkid-dev=2.36.1-6 libblkid1=2.36.1-6 libboost-chrono-dev=1.74.0.3 libboost-chrono1.74-dev=1.74.0-8 libboost-chrono1.74.0=1.74.0-8 libboost-dev=1.74.0.3 libboost-filesystem-dev=1.74.0.3 libboost-filesystem1.74-dev=1.74.0-8 libboost-filesystem1.74.0=1.74.0-8 libboost-program-options-dev=1.74.0.3 libboost-program-options1.74-dev=1.74.0-8 libboost-program-options1.74.0=1.74.0-8 libboost-random-dev=1.74.0.3 libboost-random1.74-dev=1.74.0-8 libboost-random1.74.0=1.74.0-8 libboost-system-dev=1.74.0.3 libboost-system1.74-dev=1.74.0-8 libboost-system1.74.0=1.74.0-8 libboost1.74-dev=1.74.0-8 libbrotli-dev=1.0.9-2+b2 libbrotli1=1.0.9-2+b2 libbsd0=0.11.1-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcairo-gobject2=1.16.0-5 libcairo-script-interpreter2=1.16.0-5 libcairo2=1.16.0-5 libcairo2-dev=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcmark-gfm-extensions0=0.29.0.gfm.0-6 libcmark-gfm0=0.29.0.gfm.0-6 libcom-err2=1.45.7-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.3 libdpkg-perl=1.20.7.1 libeigen3-dev=3.3.9-2 libelf1=0.182+20210205-1 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi-dev=3.3-5 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.11.0-1 libfontconfig-dev=2.13.1-4.2 libfontconfig1=2.13.1-4.2 libfontconfig1-dev=2.13.1-4.2 libfreetype-dev=2.10.4+dfsg-1 libfreetype6=2.10.4+dfsg-1 libfreetype6-dev=2.10.4+dfsg-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libglib2.0-0=2.66.6-1 libglib2.0-bin=2.66.6-1 libglib2.0-data=2.66.6-1 libglib2.0-dev=2.66.6-1 libglib2.0-dev-bin=2.66.6-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libice-dev=2:1.0.10-1 libice6=2:1.0.10-1 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 liblzo2-2=2.10-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-1 libmount-dev=2.36.1-6 libmount1=2.36.1-6 libmpc3=1.2.0-1 libmpdec3=2.5.1-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-4 libpam-modules-bin=1.4.0-4 libpam-runtime=1.4.0-4 libpam0g=1.4.0-4 libpcre16-3=2:8.39-13 libpcre2-16-0=10.36-2 libpcre2-32-0=10.36-2 libpcre2-8-0=10.36-2 libpcre2-dev=10.36-2 libpcre2-posix2=10.36-2 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.32=5.32.1-2 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpixman-1-dev=0.40.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.9.1-1 libpython3.9-minimal=3.9.1-4 libpython3.9-stdlib=3.9.1-4 libquadmath0=10.2.1-6 librange-v3-dev=0.11.0-1 libreadline8=8.1-1 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libselinux1-dev=3.1-2+b2 libsepol1=3.1-1 libsepol1-dev=3.1-1 libsigsegv2=2.13-1 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-6 libsqlite3-0=3.34.1-1 libssl1.1=1.1.1i-3 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.3-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-1 libunistring2=0.9.10-4 libuuid1=2.36.1-6 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libx11-dev=2:1.7.0-2 libxau-dev=1:1.0.9-1 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-render0-dev=1.14-3 libxcb-shm0=1.14-3 libxcb-shm0-dev=1.14-3 libxcb1=1.14-3 libxcb1-dev=1.14-3 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.3-1.1 libxext6=2:1.3.3-1.1 libxml2=2.9.10+dfsg-6.3+b1 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=4.0.0 meson=0.56.2-1 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 ninja-build=1.10.1-1 nlohmann-json3-dev=3.9.1-1 pandoc=2.9.2.1-1+b1 pandoc-data=2.9.2.1-1 patch=2.7.6-7 perl=5.32.1-2 perl-base=5.32.1-2 perl-modules-5.32=5.32.1-2 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 python3=3.9.1-1 python3-distutils=3.9.1-2 python3-lib2to3=3.9.1-2 python3-minimal=3.9.1-1 python3-pkg-resources=52.0.0-1 python3.9=3.9.1-4 python3.9-minimal=3.9.1-4 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2021a-1 ucf=3.0043 util-linux=2.36.1-6 uuid-dev=2.36.1-6 x11-common=1:7.7+21 x11proto-dev=2020.1-1 x11proto-xext-dev=2020.1-1 xorg-sgml-doctools=1:1.11-1.1 xtrans-dev=1.4.0-1 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210208T033121Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210205T151755Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d bali-phy=3.6.0+dfsg-1 && mkdir -p /build/bali-phy-kUKYaG && dpkg-source --no-check -x /*.dsc /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg && chown -R builduser:builduser /build/bali-phy-kUKYaG" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1612666578" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bali-phy-kUKYaG /tmp/bali-phy-3.6.0+dfsg-1jjjkfzxo bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210205T151755Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.w0hk_H1ON8 as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.w0hk_H1ON8 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-6). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210205T151755Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210205T151755Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1106 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210208T033121Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210205T151755Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.w0hk_H1ON8 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210205T151755Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable/main amd64 Packages [11.7 MB] Fetched 34.4 MB in 31s (1114 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.w0hk_H1ON8 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bali-phy=3.6.0+dfsg-1 && mkdir -p /build/bali-phy-kUKYaG && dpkg-source --no-check -x /*.dsc /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg && chown -R builduser:builduser /build/bali-phy-kUKYaG"' exec /tmp/mmdebstrap.w0hk_H1ON8 Reading package lists... NOTICE: 'bali-phy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bali-phy.git Please use: git clone https://salsa.debian.org/med-team/bali-phy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1129 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bali-phy 3.6.0+dfsg-1 (dsc) [2227 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bali-phy 3.6.0+dfsg-1 (tar) [1122 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main bali-phy 3.6.0+dfsg-1 (diff) [4456 B] Fetched 1129 kB in 1s (1123 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bali-phy_3.6.0+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bali-phy in /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg dpkg-source: info: unpacking bali-phy_3.6.0+dfsg.orig.tar.xz dpkg-source: info: unpacking bali-phy_3.6.0+dfsg-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1612666578" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.w0hk_H1ON8 dpkg-buildpackage: info: source package bali-phy dpkg-buildpackage: info: source version 3.6.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Benjamin Redelings dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson dh_auto_clean -O--buildsystem=meson dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary-arch dh binary-arch --buildsystem=meson dh_update_autotools_config -a -O--buildsystem=meson dh_autoreconf -a -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg' dh_auto_configure -- -Dextra-tools=false --buildtype=release -Db_ndebug=true cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dextra-tools=false --buildtype=release -Db_ndebug=true The Meson build system Version: 0.56.2 Source dir: /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg Build dir: /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: bali-phy Project version: 3.6.0 Using 'CFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' C compiler for the host machine: cc (gcc 10.2.1 "cc (Debian 10.2.1-6) 10.2.1 20210110") C linker for the host machine: cc ld.bfd 2.35.1 Using 'CXXFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.1 Using 'CFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' Using 'CXXFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' Host machine cpu family: x86_64 Host machine cpu: x86_64 Has header "sys/resource.h" : YES Has header "fenv.h" : YES Checking for function "log2" : YES Checking for function "feenableexcept" : YES Configuring config.h using configuration Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-maybe-uninitialized: YES Compiler for C++ supports arguments -Woverloaded-virtual: YES Compiler for C++ supports arguments -Wstrict-aliasing: YES Compiler for C++ supports arguments -Wno-unknown-pragmas: YES Compiler for C++ supports arguments -fdiagnostics-show-template-tree: YES Compiler for C++ supports arguments -funroll-loops: YES Compiler for C++ supports arguments -fno-math-errno: YES Compiler for C++ supports arguments -fno-signed-zeros: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency cairo found: YES 1.16.0 Run-time dependency Boost (found: chrono, filesystem, program_options, random, system) found: YES 1.74.0 (/usr) Run-time dependency eigen3 found: YES 3.3.9 Has header "nlohmann/json.hpp" : YES Library dl found: YES Has header "range/v3/view/take.hpp" : YES Library m found: YES Program pandoc found: YES (/usr/bin/pandoc) Program /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/tests/run-tests.py found: YES (/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/tests/run-tests.py) Build targets in project: 87 bali-phy 3.6.0 Architecture host: linux Libraries BOOST: system Eigen: system nlohmann::json: system range v3: system cairo: system Directories prefix: /usr Configuration optimization: 3 b_ndebug: true debug: False Found ninja-1.10.1 at /usr/bin/ninja make[1]: Leaving directory '/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg' dh_auto_build -a -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/297] /usr/bin/meson --internal vcstagger ../src/git-version.h.in src/git-version.h '' /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/src @git_message@ '(.*)' /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/src/git log -n1 '--date=format:%b %d %Y %k:%M:%S' '--pretty=format:[%D commit %h] (%cd)' [2/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_pred.cc.o -MF src/util/libutil.a.p/string_pred.cc.o.d -o src/util/libutil.a.p/string_pred.cc.o -c ../src/util/string/pred.cc [3/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/log-level.cc.o -MF src/util/libutil.a.p/log-level.cc.o.d -o src/util/libutil.a.p/log-level.cc.o -c ../src/util/log-level.cc [4/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_strip.cc.o -MF src/util/libutil.a.p/string_strip.cc.o.d -o src/util/libutil.a.p/string_strip.cc.o -c ../src/util/string/strip.cc [5/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_sanitize.cc.o -MF src/util/libutil.a.p/string_sanitize.cc.o.d -o src/util/libutil.a.p/string_sanitize.cc.o -c ../src/util/string/sanitize.cc [6/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/range.cc.o -MF src/util/libutil.a.p/range.cc.o.d -o src/util/libutil.a.p/range.cc.o -c ../src/util/range.cc [7/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/demangle.cc.o -MF src/util/libutil.a.p/demangle.cc.o.d -o src/util/libutil.a.p/demangle.cc.o -c ../src/util/demangle.cc [8/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/mapping.cc.o -MF src/util/libutil.a.p/mapping.cc.o.d -o src/util/libutil.a.p/mapping.cc.o -c ../src/util/mapping.cc [9/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/io.cc.o -MF src/util/libutil.a.p/io.cc.o.d -o src/util/libutil.a.p/io.cc.o -c ../src/util/io.cc [10/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/rng.cc.o -MF src/util/libutil.a.p/rng.cc.o.d -o src/util/libutil.a.p/rng.cc.o -c ../src/util/rng.cc [11/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/graph.cc.o -MF src/util/libutil.a.p/graph.cc.o.d -o src/util/libutil.a.p/graph.cc.o -c ../src/util/graph.cc [12/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/cmdline.cc.o -MF src/util/libutil.a.p/cmdline.cc.o.d -o src/util/libutil.a.p/cmdline.cc.o -c ../src/util/cmdline.cc [13/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/permute.cc.o -MF src/util/libutil.a.p/permute.cc.o.d -o src/util/libutil.a.p/permute.cc.o -c ../src/util/permute.cc [14/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-paths.cc.o -MF src/util/libutil.a.p/file-paths.cc.o.d -o src/util/libutil.a.p/file-paths.cc.o -c ../src/util/file-paths.cc [15/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/myexception.cc.o -MF src/util/libutil.a.p/myexception.cc.o.d -o src/util/libutil.a.p/myexception.cc.o -c ../src/util/myexception.cc [16/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/string_split.cc.o -MF src/util/libutil.a.p/string_split.cc.o.d -o src/util/libutil.a.p/string_split.cc.o -c ../src/util/string/split.cc [17/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/text.cc.o -MF src/util/libutil.a.p/text.cc.o.d -o src/util/libutil.a.p/text.cc.o -c ../src/util/text.cc [18/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_newick-tokenizer.cc.o -MF src/libcommon.a.p/tree_newick-tokenizer.cc.o.d -o src/libcommon.a.p/tree_newick-tokenizer.cc.o -c ../src/tree/newick-tokenizer.cc [19/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/time.cc.o -MF src/util/libutil.a.p/time.cc.o.d -o src/util/libutil.a.p/time.cc.o -c ../src/util/time.cc [20/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/ptree.cc.o -MF src/util/libutil.a.p/ptree.cc.o.d -o src/util/libutil.a.p/ptree.cc.o -c ../src/util/ptree.cc [21/297] c++ -Isrc/util/libutil.a.p -Isrc/util -I../src/util -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/util/libutil.a.p/file-readers.cc.o -MF src/util/libutil.a.p/file-readers.cc.o.d -o src/util/libutil.a.p/file-readers.cc.o -c ../src/util/file-readers.cc [22/297] rm -f src/util/libutil.a && gcc-ar csrD src/util/libutil.a src/util/libutil.a.p/string_pred.cc.o src/util/libutil.a.p/string_sanitize.cc.o src/util/libutil.a.p/string_strip.cc.o src/util/libutil.a.p/string_split.cc.o src/util/libutil.a.p/log-level.cc.o src/util/libutil.a.p/io.cc.o src/util/libutil.a.p/graph.cc.o src/util/libutil.a.p/range.cc.o src/util/libutil.a.p/demangle.cc.o src/util/libutil.a.p/mapping.cc.o src/util/libutil.a.p/cmdline.cc.o src/util/libutil.a.p/rng.cc.o src/util/libutil.a.p/permute.cc.o src/util/libutil.a.p/file-paths.cc.o src/util/libutil.a.p/ptree.cc.o src/util/libutil.a.p/text.cc.o src/util/libutil.a.p/myexception.cc.o src/util/libutil.a.p/time.cc.o src/util/libutil.a.p/file-readers.cc.o [23/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_sequencetree.cc.o -MF src/libcommon.a.p/tree_sequencetree.cc.o.d -o src/libcommon.a.p/tree_sequencetree.cc.o -c ../src/tree/sequencetree.cc [24/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_randomtree.cc.o -MF src/libcommon.a.p/tree_randomtree.cc.o.d -o src/libcommon.a.p/tree_randomtree.cc.o -c ../src/tree/randomtree.cc [25/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_n_indels.cc.o -MF src/libcommon.a.p/tree-align_n_indels.cc.o.d -o src/libcommon.a.p/tree-align_n_indels.cc.o -c ../src/tree-align/n_indels.cc [26/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_tree-util.cc.o -MF src/libcommon.a.p/tree_tree-util.cc.o.d -o src/libcommon.a.p/tree_tree-util.cc.o -c ../src/tree/tree-util.cc [27/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_sequence-format.cc.o -MF src/libcommon.a.p/sequence_sequence-format.cc.o.d -o src/libcommon.a.p/sequence_sequence-format.cc.o -c ../src/sequence/sequence-format.cc [28/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree_tree.cc.o -MF src/libcommon.a.p/tree_tree.cc.o.d -o src/libcommon.a.p/tree_tree.cc.o -c ../src/tree/tree.cc [29/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_sequence.cc.o -MF src/libcommon.a.p/sequence_sequence.cc.o.d -o src/libcommon.a.p/sequence_sequence.cc.o -c ../src/sequence/sequence.cc [30/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_read-trees.cc.o -MF src/libcommon.a.p/tools_read-trees.cc.o.d -o src/libcommon.a.p/tools_read-trees.cc.o -c ../src/tools/read-trees.cc [31/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/sequence_alphabet.cc.o -MF src/libcommon.a.p/sequence_alphabet.cc.o.d -o src/libcommon.a.p/sequence_alphabet.cc.o -c ../src/sequence/alphabet.cc [32/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-util.cc.o -MF src/libcommon.a.p/alignment_alignment-util.cc.o.d -o src/libcommon.a.p/alignment_alignment-util.cc.o -c ../src/alignment/alignment-util.cc [33/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment-random.cc.o -MF src/libcommon.a.p/alignment_alignment-random.cc.o.d -o src/libcommon.a.p/alignment_alignment-random.cc.o -c ../src/alignment/alignment-random.cc [34/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tree-align_link.cc.o -MF src/libcommon.a.p/tree-align_link.cc.o.d -o src/libcommon.a.p/tree-align_link.cc.o -c ../src/tree-align/link.cc [35/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_load.cc.o -MF src/libcommon.a.p/alignment_load.cc.o.d -o src/libcommon.a.p/alignment_load.cc.o -c ../src/alignment/load.cc [36/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_statistics.cc.o -MF src/libcommon.a.p/tools_statistics.cc.o.d -o src/libcommon.a.p/tools_statistics.cc.o -c ../src/tools/statistics.cc [37/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/models_path.cc.o -MF src/libcommon.a.p/models_path.cc.o.d -o src/libcommon.a.p/models_path.cc.o -c ../src/models/path.cc [38/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_index-matrix.cc.o -MF src/libcommon.a.p/alignment_index-matrix.cc.o.d -o src/libcommon.a.p/alignment_index-matrix.cc.o -c ../src/alignment/index-matrix.cc [39/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/alignment_alignment.cc.o -MF src/libcommon.a.p/alignment_alignment.cc.o.d -o src/libcommon.a.p/alignment_alignment.cc.o -c ../src/alignment/alignment.cc [40/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_parsimony.cc.o -MF src/libcommon.a.p/tools_parsimony.cc.o.d -o src/libcommon.a.p/tools_parsimony.cc.o -c ../src/tools/parsimony.cc [41/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_partition.cc.o -MF src/libcommon.a.p/tools_partition.cc.o.d -o src/libcommon.a.p/tools_partition.cc.o -c ../src/tools/partition.cc [42/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_tree-dist.cc.o -MF src/libcommon.a.p/tools_tree-dist.cc.o.d -o src/libcommon.a.p/tools_tree-dist.cc.o -c ../src/tools/tree-dist.cc [43/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_findroot.cc.o -MF src/libcommon.a.p/tools_findroot.cc.o.d -o src/libcommon.a.p/tools_findroot.cc.o -c ../src/tools/findroot.cc [44/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_mctree.cc.o -MF src/libcommon.a.p/tools_mctree.cc.o.d -o src/libcommon.a.p/tools_mctree.cc.o -c ../src/tools/mctree.cc [45/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_optimize.cc.o -MF src/libcommon.a.p/tools_optimize.cc.o.d -o src/libcommon.a.p/tools_optimize.cc.o -c ../src/tools/optimize.cc [46/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_distance-report.cc.o -MF src/libcommon.a.p/tools_distance-report.cc.o.d -o src/libcommon.a.p/tools_distance-report.cc.o -c ../src/tools/distance-report.cc [47/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_stats-table.cc.o -MF src/libcommon.a.p/tools_stats-table.cc.o.d -o src/libcommon.a.p/tools_stats-table.cc.o -c ../src/tools/stats-table.cc [48/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_distance-methods.cc.o -MF src/libcommon.a.p/tools_distance-methods.cc.o.d -o src/libcommon.a.p/tools_distance-methods.cc.o -c ../src/tools/distance-methods.cc [49/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_inverse.cc.o -MF src/libcommon.a.p/tools_inverse.cc.o.d -o src/libcommon.a.p/tools_inverse.cc.o -c ../src/tools/inverse.cc [50/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/object.cc.o -MF src/computation/libcomputation.a.p/object.cc.o.d -o src/computation/libcomputation.a.p/object.cc.o -c ../src/computation/object.cc [51/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/closure.cc.o -MF src/computation/libcomputation.a.p/closure.cc.o.d -o src/computation/libcomputation.a.p/closure.cc.o -c ../src/computation/closure.cc [52/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_consensus-tree.cc.o -MF src/libcommon.a.p/tools_consensus-tree.cc.o.d -o src/libcommon.a.p/tools_consensus-tree.cc.o -c ../src/tools/consensus-tree.cc [53/297] c++ -Isrc/libcommon.a.p -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libcommon.a.p/tools_joint-A-T.cc.o -MF src/libcommon.a.p/tools_joint-A-T.cc.o.d -o src/libcommon.a.p/tools_joint-A-T.cc.o -c ../src/tools/joint-A-T.cc [54/297] rm -f src/libcommon.a && gcc-ar csrD src/libcommon.a src/libcommon.a.p/tree_newick-tokenizer.cc.o src/libcommon.a.p/tree_sequencetree.cc.o src/libcommon.a.p/tree_tree.cc.o src/libcommon.a.p/tree_tree-util.cc.o src/libcommon.a.p/tree_randomtree.cc.o src/libcommon.a.p/tree-align_n_indels.cc.o src/libcommon.a.p/sequence_alphabet.cc.o src/libcommon.a.p/sequence_sequence.cc.o src/libcommon.a.p/sequence_sequence-format.cc.o src/libcommon.a.p/tools_read-trees.cc.o src/libcommon.a.p/alignment_alignment-util.cc.o src/libcommon.a.p/alignment_load.cc.o src/libcommon.a.p/alignment_alignment.cc.o src/libcommon.a.p/alignment_alignment-random.cc.o src/libcommon.a.p/alignment_index-matrix.cc.o src/libcommon.a.p/tree-align_link.cc.o src/libcommon.a.p/models_path.cc.o src/libcommon.a.p/tools_statistics.cc.o src/libcommon.a.p/tools_partition.cc.o src/libcommon.a.p/tools_tree-dist.cc.o src/libcommon.a.p/tools_parsimony.cc.o src/libcommon.a.p/tools_mctree.cc.o src/libcommon.a.p/tools_stats-table.cc.o src/libcommon.a.p/tools_findroot.cc.o src/libcommon.a.p/tools_optimize.cc.o src/libcommon.a.p/tools_distance-report.cc.o src/libcommon.a.p/tools_inverse.cc.o src/libcommon.a.p/tools_joint-A-T.cc.o src/libcommon.a.p/tools_distance-methods.cc.o src/libcommon.a.p/tools_consensus-tree.cc.o [55/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/preprocess.cc.o -MF src/computation/libcomputation.a.p/preprocess.cc.o.d -o src/computation/libcomputation.a.p/preprocess.cc.o -c ../src/computation/preprocess.cc [56/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/program.cc.o -MF src/computation/libcomputation.a.p/program.cc.o.d -o src/computation/libcomputation.a.p/program.cc.o -c ../src/computation/program.cc ../src/computation/program.cc: In member function ‘void Program::check_dependencies()’: ../src/computation/program.cc:155:10: warning: unused variable ‘index’ [-Wunused-variable] 155 | int index = find_module(name); | ^~~~~ [57/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/context.cc.o -MF src/computation/libcomputation.a.p/context.cc.o.d -o src/computation/libcomputation.a.p/context.cc.o -c ../src/computation/context.cc [58/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/operations.cc.o -MF src/computation/libcomputation.a.p/operations.cc.o.d -o src/computation/libcomputation.a.p/operations.cc.o -c ../src/computation/operations.cc [59/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/param.cc.o -MF src/computation/libcomputation.a.p/param.cc.o.d -o src/computation/libcomputation.a.p/param.cc.o -c ../src/computation/param.cc [60/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/loader.cc.o -MF src/computation/libcomputation.a.p/loader.cc.o.d -o src/computation/libcomputation.a.p/loader.cc.o -c ../src/computation/loader.cc [61/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/module.cc.o -MF src/computation/libcomputation.a.p/module.cc.o.d -o src/computation/libcomputation.a.p/module.cc.o -c ../src/computation/module.cc [62/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_driver.cc.o -MF src/computation/libcomputation.a.p/parser_driver.cc.o.d -o src/computation/libcomputation.a.p/parser_driver.cc.o -c ../src/computation/parser/driver.cc [63/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_desugar.cc.o -MF src/computation/libcomputation.a.p/parser_desugar.cc.o.d -o src/computation/libcomputation.a.p/parser_desugar.cc.o -c ../src/computation/parser/desugar.cc [64/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_rename.cc.o -MF src/computation/libcomputation.a.p/parser_rename.cc.o.d -o src/computation/libcomputation.a.p/parser_rename.cc.o -c ../src/computation/parser/rename.cc [65/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_desugar-case.cc.o -MF src/computation/libcomputation.a.p/parser_desugar-case.cc.o.d -o src/computation/libcomputation.a.p/parser_desugar-case.cc.o -c ../src/computation/parser/desugar-case.cc [66/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_lexer.cc.o -MF src/computation/libcomputation.a.p/parser_lexer.cc.o.d -o src/computation/libcomputation.a.p/parser_lexer.cc.o -c ../src/computation/parser/lexer.cc [67/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_operator.cc.o -MF src/computation/libcomputation.a.p/expression_operator.cc.o.d -o src/computation/libcomputation.a.p/expression_operator.cc.o -c ../src/computation/expression/operator.cc [68/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_constructor.cc.o -MF src/computation/libcomputation.a.p/expression_constructor.cc.o.d -o src/computation/libcomputation.a.p/expression_constructor.cc.o -c ../src/computation/expression/constructor.cc [69/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_expression.cc.o -MF src/computation/libcomputation.a.p/expression_expression.cc.o.d -o src/computation/libcomputation.a.p/expression_expression.cc.o -c ../src/computation/expression/expression.cc [70/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_AST_node.cc.o -MF src/computation/libcomputation.a.p/expression_AST_node.cc.o.d -o src/computation/libcomputation.a.p/expression_AST_node.cc.o -c ../src/computation/expression/AST_node.cc [71/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_apply.cc.o -MF src/computation/libcomputation.a.p/expression_apply.cc.o.d -o src/computation/libcomputation.a.p/expression_apply.cc.o -c ../src/computation/expression/apply.cc [72/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/parser_parser.cc.o -MF src/computation/libcomputation.a.p/parser_parser.cc.o.d -o src/computation/libcomputation.a.p/parser_parser.cc.o -c ../src/computation/parser/parser.cc [73/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/substitution_substitution.cc.o -MF src/libbaliphy.a.p/substitution_substitution.cc.o.d -o src/libbaliphy.a.p/substitution_substitution.cc.o -c ../src/substitution/substitution.cc [74/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_expression_ref.cc.o -MF src/computation/libcomputation.a.p/expression_expression_ref.cc.o.d -o src/computation/libcomputation.a.p/expression_expression_ref.cc.o -c ../src/computation/expression/expression_ref.cc [75/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_substitute.cc.o -MF src/computation/libcomputation.a.p/expression_substitute.cc.o.d -o src/computation/libcomputation.a.p/expression_substitute.cc.o -c ../src/computation/expression/substitute.cc [76/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_indexify.cc.o -MF src/computation/libcomputation.a.p/expression_indexify.cc.o.d -o src/computation/libcomputation.a.p/expression_indexify.cc.o -c ../src/computation/expression/indexify.cc [77/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_case.cc.o -MF src/computation/libcomputation.a.p/expression_case.cc.o.d -o src/computation/libcomputation.a.p/expression_case.cc.o -c ../src/computation/expression/case.cc [78/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_tuple.cc.o -MF src/computation/libcomputation.a.p/expression_tuple.cc.o.d -o src/computation/libcomputation.a.p/expression_tuple.cc.o -c ../src/computation/expression/tuple.cc [79/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_let.cc.o -MF src/computation/libcomputation.a.p/expression_let.cc.o.d -o src/computation/libcomputation.a.p/expression_let.cc.o -c ../src/computation/expression/let.cc [80/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_trim.cc.o -MF src/computation/libcomputation.a.p/expression_trim.cc.o.d -o src/computation/libcomputation.a.p/expression_trim.cc.o -c ../src/computation/expression/trim.cc [81/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_lambda.cc.o -MF src/computation/libcomputation.a.p/expression_lambda.cc.o.d -o src/computation/libcomputation.a.p/expression_lambda.cc.o -c ../src/computation/expression/lambda.cc [82/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_var.cc.o -MF src/computation/libcomputation.a.p/expression_var.cc.o.d -o src/computation/libcomputation.a.p/expression_var.cc.o -c ../src/computation/expression/var.cc [83/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_list.cc.o -MF src/computation/libcomputation.a.p/expression_list.cc.o.d -o src/computation/libcomputation.a.p/expression_list.cc.o -c ../src/computation/expression/list.cc [84/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_reg_var.cc.o -MF src/computation/libcomputation.a.p/expression_reg_var.cc.o.d -o src/computation/libcomputation.a.p/expression_reg_var.cc.o -c ../src/computation/expression/reg_var.cc [85/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_random_variable.cc.o -MF src/computation/libcomputation.a.p/expression_random_variable.cc.o.d -o src/computation/libcomputation.a.p/expression_random_variable.cc.o -c ../src/computation/expression/random_variable.cc [86/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_modifiable.cc.o -MF src/computation/libcomputation.a.p/expression_modifiable.cc.o.d -o src/computation/libcomputation.a.p/expression_modifiable.cc.o -c ../src/computation/expression/modifiable.cc [87/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_bool.cc.o -MF src/computation/libcomputation.a.p/expression_bool.cc.o.d -o src/computation/libcomputation.a.p/expression_bool.cc.o -c ../src/computation/expression/bool.cc [88/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o -MF src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o.d -o src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o -c ../src/computation/expression/resolved_symbol.cc [89/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_maybe.cc.o -MF src/computation/libcomputation.a.p/expression_maybe.cc.o.d -o src/computation/libcomputation.a.p/expression_maybe.cc.o -c ../src/computation/expression/maybe.cc [90/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_args.cc.o -MF src/computation/libcomputation.a.p/machine_args.cc.o.d -o src/computation/libcomputation.a.p/machine_args.cc.o -c ../src/computation/machine/args.cc [91/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_do_block.cc.o -MF src/computation/libcomputation.a.p/expression_do_block.cc.o.d -o src/computation/libcomputation.a.p/expression_do_block.cc.o -c ../src/computation/expression/do_block.cc [92/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_tokens.cc.o -MF src/computation/libcomputation.a.p/machine_tokens.cc.o.d -o src/computation/libcomputation.a.p/machine_tokens.cc.o -c ../src/computation/machine/tokens.cc [93/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_sums.cc.o -MF src/computation/libcomputation.a.p/machine_sums.cc.o.d -o src/computation/libcomputation.a.p/machine_sums.cc.o -c ../src/computation/machine/sums.cc [94/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_evaluate.cc.o -MF src/computation/libcomputation.a.p/machine_evaluate.cc.o.d -o src/computation/libcomputation.a.p/machine_evaluate.cc.o -c ../src/computation/machine/evaluate.cc [95/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_gc.cc.o -MF src/computation/libcomputation.a.p/machine_gc.cc.o.d -o src/computation/libcomputation.a.p/machine_gc.cc.o -c ../src/computation/machine/gc.cc [96/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_show_graph.cc.o -MF src/computation/libcomputation.a.p/machine_show_graph.cc.o.d -o src/computation/libcomputation.a.p/machine_show_graph.cc.o -c ../src/computation/machine/show_graph.cc [97/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_reroot.cc.o -MF src/computation/libcomputation.a.p/machine_reroot.cc.o.d -o src/computation/libcomputation.a.p/machine_reroot.cc.o -c ../src/computation/machine/reroot.cc [98/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/expression_kind.cc.o -MF src/computation/libcomputation.a.p/expression_kind.cc.o.d -o src/computation/libcomputation.a.p/expression_kind.cc.o -c ../src/computation/expression/kind.cc [99/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_effects.cc.o -MF src/computation/libcomputation.a.p/machine_effects.cc.o.d -o src/computation/libcomputation.a.p/machine_effects.cc.o -c ../src/computation/machine/effects.cc [100/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/machine_graph_register.cc.o -MF src/computation/libcomputation.a.p/machine_graph_register.cc.o.d -o src/computation/libcomputation.a.p/machine_graph_register.cc.o -c ../src/computation/machine/graph_register.cc [101/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_free-vars.cc.o -MF src/computation/libcomputation.a.p/optimization_free-vars.cc.o.d -o src/computation/libcomputation.a.p/optimization_free-vars.cc.o -c ../src/computation/optimization/free-vars.cc [102/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_inliner.cc.o -MF src/computation/libcomputation.a.p/optimization_inliner.cc.o.d -o src/computation/libcomputation.a.p/optimization_inliner.cc.o -c ../src/computation/optimization/inliner.cc [103/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_float-out.cc.o -MF src/computation/libcomputation.a.p/optimization_float-out.cc.o.d -o src/computation/libcomputation.a.p/optimization_float-out.cc.o -c ../src/computation/optimization/float-out.cc [104/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_set-levels.cc.o -MF src/computation/libcomputation.a.p/optimization_set-levels.cc.o.d -o src/computation/libcomputation.a.p/optimization_set-levels.cc.o -c ../src/computation/optimization/set-levels.cc [105/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_occurrence.cc.o -MF src/computation/libcomputation.a.p/optimization_occurrence.cc.o.d -o src/computation/libcomputation.a.p/optimization_occurrence.cc.o -c ../src/computation/optimization/occurrence.cc [106/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp_hmm.cc.o -MF src/libbaliphy.a.p/dp_dp_hmm.cc.o.d -o src/libbaliphy.a.p/dp_dp_hmm.cc.o -c ../src/dp/dp_hmm.cc [107/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-engine.cc.o -MF src/libbaliphy.a.p/dp_dp-engine.cc.o.d -o src/libbaliphy.a.p/dp_dp-engine.cc.o -c ../src/dp/dp-engine.cc [108/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-array.cc.o -MF src/libbaliphy.a.p/dp_dp-array.cc.o.d -o src/libbaliphy.a.p/dp_dp-array.cc.o -c ../src/dp/dp-array.cc [109/297] c++ -Isrc/computation/libcomputation.a.p -Isrc/computation -I../src/computation -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -isystem../external/immer -isystemexternal/immer/ -MD -MQ src/computation/libcomputation.a.p/optimization_simplifier.cc.o -MF src/computation/libcomputation.a.p/optimization_simplifier.cc.o.d -o src/computation/libcomputation.a.p/optimization_simplifier.cc.o -c ../src/computation/optimization/simplifier.cc [110/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-matrix.cc.o -MF src/libbaliphy.a.p/dp_dp-matrix.cc.o.d -o src/libbaliphy.a.p/dp_dp-matrix.cc.o -c ../src/dp/dp-matrix.cc [111/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_hmm.cc.o -MF src/libbaliphy.a.p/dp_hmm.cc.o.d -o src/libbaliphy.a.p/dp_hmm.cc.o -c ../src/dp/hmm.cc [112/297] rm -f src/computation/libcomputation.a && gcc-ar csrD src/computation/libcomputation.a src/computation/libcomputation.a.p/object.cc.o src/computation/libcomputation.a.p/closure.cc.o src/computation/libcomputation.a.p/program.cc.o src/computation/libcomputation.a.p/preprocess.cc.o src/computation/libcomputation.a.p/module.cc.o src/computation/libcomputation.a.p/loader.cc.o src/computation/libcomputation.a.p/context.cc.o src/computation/libcomputation.a.p/operations.cc.o src/computation/libcomputation.a.p/param.cc.o src/computation/libcomputation.a.p/parser_desugar.cc.o src/computation/libcomputation.a.p/parser_desugar-case.cc.o src/computation/libcomputation.a.p/parser_rename.cc.o src/computation/libcomputation.a.p/parser_driver.cc.o src/computation/libcomputation.a.p/parser_lexer.cc.o src/computation/libcomputation.a.p/parser_parser.cc.o src/computation/libcomputation.a.p/expression_operator.cc.o src/computation/libcomputation.a.p/expression_expression.cc.o src/computation/libcomputation.a.p/expression_constructor.cc.o src/computation/libcomputation.a.p/expression_expression_ref.cc.o src/computation/libcomputation.a.p/expression_AST_node.cc.o src/computation/libcomputation.a.p/expression_apply.cc.o src/computation/libcomputation.a.p/expression_substitute.cc.o src/computation/libcomputation.a.p/expression_indexify.cc.o src/computation/libcomputation.a.p/expression_let.cc.o src/computation/libcomputation.a.p/expression_case.cc.o src/computation/libcomputation.a.p/expression_trim.cc.o src/computation/libcomputation.a.p/expression_tuple.cc.o src/computation/libcomputation.a.p/expression_list.cc.o src/computation/libcomputation.a.p/expression_var.cc.o src/computation/libcomputation.a.p/expression_lambda.cc.o src/computation/libcomputation.a.p/expression_random_variable.cc.o src/computation/libcomputation.a.p/expression_modifiable.cc.o src/computation/libcomputation.a.p/expression_reg_var.cc.o src/computation/libcomputation.a.p/expression_bool.cc.o src/computation/libcomputation.a.p/expression_resolved_symbol.cc.o src/computation/libcomputation.a.p/expression_maybe.cc.o src/computation/libcomputation.a.p/expression_do_block.cc.o src/computation/libcomputation.a.p/machine_args.cc.o src/computation/libcomputation.a.p/machine_tokens.cc.o src/computation/libcomputation.a.p/machine_graph_register.cc.o src/computation/libcomputation.a.p/machine_show_graph.cc.o src/computation/libcomputation.a.p/machine_evaluate.cc.o src/computation/libcomputation.a.p/machine_sums.cc.o src/computation/libcomputation.a.p/machine_gc.cc.o src/computation/libcomputation.a.p/machine_reroot.cc.o src/computation/libcomputation.a.p/machine_effects.cc.o src/computation/libcomputation.a.p/expression_kind.cc.o src/computation/libcomputation.a.p/optimization_free-vars.cc.o src/computation/libcomputation.a.p/optimization_set-levels.cc.o src/computation/libcomputation.a.p/optimization_float-out.cc.o src/computation/libcomputation.a.p/optimization_occurrence.cc.o src/computation/libcomputation.a.p/optimization_inliner.cc.o src/computation/libcomputation.a.p/optimization_simplifier.cc.o [113/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_dp-cube.cc.o -MF src/libbaliphy.a.p/dp_dp-cube.cc.o.d -o src/libbaliphy.a.p/dp_dp-cube.cc.o -c ../src/dp/dp-cube.cc [114/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_3way.cc.o -MF src/libbaliphy.a.p/dp_3way.cc.o.d -o src/libbaliphy.a.p/dp_3way.cc.o -c ../src/dp/3way.cc [115/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_5way.cc.o -MF src/libbaliphy.a.p/dp_5way.cc.o.d -o src/libbaliphy.a.p/dp_5way.cc.o -c ../src/dp/5way.cc [116/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_2way.cc.o -MF src/libbaliphy.a.p/dp_2way.cc.o.d -o src/libbaliphy.a.p/dp_2way.cc.o -c ../src/dp/2way.cc [117/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/dp_alignment-sums.cc.o -MF src/libbaliphy.a.p/dp_alignment-sums.cc.o.d -o src/libbaliphy.a.p/dp_alignment-sums.cc.o -c ../src/dp/alignment-sums.cc [118/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_AIS.cc.o -MF src/libbaliphy.a.p/mcmc_AIS.cc.o.d -o src/libbaliphy.a.p/mcmc_AIS.cc.o -c ../src/mcmc/AIS.cc [119/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_slice-sampling.cc.o -MF src/libbaliphy.a.p/mcmc_slice-sampling.cc.o.d -o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o -c ../src/mcmc/slice-sampling.cc [120/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_proposals.cc.o -MF src/libbaliphy.a.p/mcmc_proposals.cc.o.d -o src/libbaliphy.a.p/mcmc_proposals.cc.o -c ../src/mcmc/proposals.cc [121/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_mcmc.cc.o -MF src/libbaliphy.a.p/mcmc_mcmc.cc.o.d -o src/libbaliphy.a.p/mcmc_mcmc.cc.o -c ../src/mcmc/mcmc.cc [122/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_moves.cc.o -MF src/libbaliphy.a.p/mcmc_moves.cc.o.d -o src/libbaliphy.a.p/mcmc_moves.cc.o -c ../src/mcmc/moves.cc [123/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-alignment.cc.o -MF src/libbaliphy.a.p/mcmc_sample-alignment.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-alignment.cc.o -c ../src/mcmc/sample-alignment.cc [124/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -MF src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o -c ../src/mcmc/sample-branch-lengths.cc [125/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_logger.cc.o -MF src/libbaliphy.a.p/mcmc_logger.cc.o.d -o src/libbaliphy.a.p/mcmc_logger.cc.o -c ../src/mcmc/logger.cc [126/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o -MF src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o -c ../src/mcmc/sample-two-nodes.cc [127/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o -MF src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o -c ../src/mcmc/sample-topology-NNI.cc [128/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o -MF src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o -c ../src/mcmc/sample-topology-SPR.cc [129/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-node.cc.o -MF src/libbaliphy.a.p/mcmc_sample-node.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-node.cc.o -c ../src/mcmc/sample-node.cc [130/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-cube.cc.o -MF src/libbaliphy.a.p/mcmc_sample-cube.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-cube.cc.o -c ../src/mcmc/sample-cube.cc [131/297] /usr/bin/meson --internal exe --capture doc/cut-range.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/cut-range.md [132/297] /usr/bin/meson --internal exe --capture doc/pickout.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/pickout.md [133/297] /usr/bin/meson --internal exe --capture doc/trees-distances.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/trees-distances.md [134/297] /usr/bin/meson --internal exe --capture doc/alignment-thin.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-thin.md [135/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_exponential.cc.o -MF src/libbaliphy.a.p/math_exponential.cc.o.d -o src/libbaliphy.a.p/math_exponential.cc.o -c ../src/math/exponential.cc [136/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_sample-tri.cc.o -MF src/libbaliphy.a.p/mcmc_sample-tri.cc.o.d -o src/libbaliphy.a.p/mcmc_sample-tri.cc.o -c ../src/mcmc/sample-tri.cc [137/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_pow2.cc.o -MF src/libbaliphy.a.p/math_pow2.cc.o.d -o src/libbaliphy.a.p/math_pow2.cc.o -c ../src/math/pow2.cc [138/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/substitution_parsimony.cc.o -MF src/libbaliphy.a.p/substitution_parsimony.cc.o.d -o src/libbaliphy.a.p/substitution_parsimony.cc.o -c ../src/substitution/parsimony.cc [139/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/mcmc_setup.cc.o -MF src/libbaliphy.a.p/mcmc_setup.cc.o.d -o src/libbaliphy.a.p/mcmc_setup.cc.o -c ../src/mcmc/setup.cc [140/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_site-compression.cc.o -MF src/libbaliphy.a.p/models_site-compression.cc.o.d -o src/libbaliphy.a.p/models_site-compression.cc.o -c ../src/models/site-compression.cc [141/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/math_eigenvalue.cc.o -MF src/libbaliphy.a.p/math_eigenvalue.cc.o.d -o src/libbaliphy.a.p/math_eigenvalue.cc.o -c ../src/math/eigenvalue.cc [142/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_TreeInterface.cc.o -MF src/libbaliphy.a.p/models_TreeInterface.cc.o.d -o src/libbaliphy.a.p/models_TreeInterface.cc.o -c ../src/models/TreeInterface.cc [143/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_rules.cc.o -MF src/libbaliphy.a.p/models_rules.cc.o.d -o src/libbaliphy.a.p/models_rules.cc.o -c ../src/models/rules.cc [144/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parse.cc.o -MF src/libbaliphy.a.p/models_parse.cc.o.d -o src/libbaliphy.a.p/models_parse.cc.o -c ../src/models/parse.cc [145/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_parameters.cc.o -MF src/libbaliphy.a.p/models_parameters.cc.o.d -o src/libbaliphy.a.p/models_parameters.cc.o -c ../src/models/parameters.cc [146/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_setup.cc.o -MF src/libbaliphy.a.p/models_setup.cc.o.d -o src/libbaliphy.a.p/models_setup.cc.o -c ../src/models/setup.cc [147/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_unification.cc.o -MF src/libbaliphy.a.p/models_unification.cc.o.d -o src/libbaliphy.a.p/models_unification.cc.o -c ../src/models/unification.cc [148/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_typecheck.cc.o -MF src/libbaliphy.a.p/models_typecheck.cc.o.d -o src/libbaliphy.a.p/models_typecheck.cc.o -c ../src/models/typecheck.cc [149/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_link2.cc.o -MF src/libbaliphy.a.p/tree-align_link2.cc.o.d -o src/libbaliphy.a.p/tree-align_link2.cc.o -c ../src/tree-align/link2.cc [150/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_choose.cc.o -MF src/libbaliphy.a.p/probability_choose.cc.o.d -o src/libbaliphy.a.p/probability_choose.cc.o -c ../src/probability/choose.cc [151/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -MF src/libbaliphy.a.p/alignment_alignment-constraint.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o -c ../src/alignment/alignment-constraint.cc [152/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/imodel_imodel.cc.o -MF src/libbaliphy.a.p/imodel_imodel.cc.o.d -o src/libbaliphy.a.p/imodel_imodel.cc.o -c ../src/imodel/imodel.cc [153/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tree-align_n_indels2.cc.o -MF src/libbaliphy.a.p/tree-align_n_indels2.cc.o.d -o src/libbaliphy.a.p/tree-align_n_indels2.cc.o -c ../src/tree-align/n_indels2.cc [154/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/probability_probability.cc.o -MF src/libbaliphy.a.p/probability_probability.cc.o.d -o src/libbaliphy.a.p/probability_probability.cc.o -c ../src/probability/probability.cc [155/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/models_model.cc.o -MF src/libbaliphy.a.p/models_model.cc.o.d -o src/libbaliphy.a.p/models_model.cc.o -c ../src/models/model.cc [156/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/alignment_alignment-util2.cc.o -MF src/libbaliphy.a.p/alignment_alignment-util2.cc.o.d -o src/libbaliphy.a.p/alignment_alignment-util2.cc.o -c ../src/alignment/alignment-util2.cc [157/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/version.cc.o -MF src/libbaliphy.a.p/version.cc.o.d -o src/libbaliphy.a.p/version.cc.o -c ../src/version.cc ../src/version.cc:67:8: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 67 | s<<__DATE__<<" "<<__TIME__; | ^~~~~~~~ ../src/version.cc:67:23: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 67 | s<<__DATE__<<" "<<__TIME__; | ^~~~~~~~ [158/297] c++ -Isrc/builtins/Data.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Data.so.p/Data.cc.o -MF src/builtins/Data.so.p/Data.cc.o.d -o src/builtins/Data.so.p/Data.cc.o -c ../src/builtins/Data.cc [159/297] c++ -Isrc/libbaliphy.a.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/libbaliphy.a.p/tools_parsimony2.cc.o -MF src/libbaliphy.a.p/tools_parsimony2.cc.o.d -o src/libbaliphy.a.p/tools_parsimony2.cc.o -c ../src/tools/parsimony2.cc [160/297] rm -f src/libbaliphy.a && gcc-ar csrD src/libbaliphy.a src/libbaliphy.a.p/dp_dp_hmm.cc.o src/libbaliphy.a.p/dp_hmm.cc.o src/libbaliphy.a.p/dp_dp-engine.cc.o src/libbaliphy.a.p/dp_dp-array.cc.o src/libbaliphy.a.p/dp_dp-matrix.cc.o src/libbaliphy.a.p/dp_dp-cube.cc.o src/libbaliphy.a.p/dp_2way.cc.o src/libbaliphy.a.p/dp_3way.cc.o src/libbaliphy.a.p/dp_5way.cc.o src/libbaliphy.a.p/dp_alignment-sums.cc.o src/libbaliphy.a.p/mcmc_mcmc.cc.o src/libbaliphy.a.p/mcmc_proposals.cc.o src/libbaliphy.a.p/mcmc_slice-sampling.cc.o src/libbaliphy.a.p/mcmc_AIS.cc.o src/libbaliphy.a.p/mcmc_logger.cc.o src/libbaliphy.a.p/mcmc_moves.cc.o src/libbaliphy.a.p/mcmc_sample-branch-lengths.cc.o src/libbaliphy.a.p/mcmc_sample-alignment.cc.o src/libbaliphy.a.p/mcmc_sample-topology-SPR.cc.o src/libbaliphy.a.p/mcmc_sample-topology-NNI.cc.o src/libbaliphy.a.p/mcmc_sample-two-nodes.cc.o src/libbaliphy.a.p/mcmc_sample-node.cc.o src/libbaliphy.a.p/mcmc_sample-cube.cc.o src/libbaliphy.a.p/mcmc_sample-tri.cc.o src/libbaliphy.a.p/mcmc_setup.cc.o src/libbaliphy.a.p/substitution_substitution.cc.o src/libbaliphy.a.p/substitution_parsimony.cc.o src/libbaliphy.a.p/math_exponential.cc.o src/libbaliphy.a.p/math_eigenvalue.cc.o src/libbaliphy.a.p/math_pow2.cc.o src/libbaliphy.a.p/models_parameters.cc.o src/libbaliphy.a.p/models_site-compression.cc.o src/libbaliphy.a.p/models_TreeInterface.cc.o src/libbaliphy.a.p/models_setup.cc.o src/libbaliphy.a.p/models_rules.cc.o src/libbaliphy.a.p/models_parse.cc.o src/libbaliphy.a.p/models_typecheck.cc.o src/libbaliphy.a.p/models_unification.cc.o src/libbaliphy.a.p/models_model.cc.o src/libbaliphy.a.p/tree-align_link2.cc.o src/libbaliphy.a.p/probability_choose.cc.o src/libbaliphy.a.p/probability_probability.cc.o src/libbaliphy.a.p/imodel_imodel.cc.o src/libbaliphy.a.p/alignment_alignment-constraint.cc.o src/libbaliphy.a.p/alignment_alignment-util2.cc.o src/libbaliphy.a.p/tree-align_n_indels2.cc.o src/libbaliphy.a.p/tools_parsimony2.cc.o src/libbaliphy.a.p/version.cc.o [161/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/link-partitions.cc.o -MF src/bali-phy/bali-phy.p/link-partitions.cc.o.d -o src/bali-phy/bali-phy.p/link-partitions.cc.o -c ../src/bali-phy/link-partitions.cc [162/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/bali-phy.cc.o -MF src/bali-phy/bali-phy.p/bali-phy.cc.o.d -o src/bali-phy/bali-phy.p/bali-phy.cc.o -c ../src/bali-phy/bali-phy.cc ../src/bali-phy/bali-phy.cc: In function ‘void report_mem()’: ../src/bali-phy/bali-phy.cc:122:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 122 | system(cmd.str().c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~ [163/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/files.cc.o -MF src/bali-phy/bali-phy.p/files.cc.o.d -o src/bali-phy/bali-phy.p/files.cc.o -c ../src/bali-phy/files.cc [164/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/help.cc.o -MF src/bali-phy/bali-phy.p/help.cc.o.d -o src/bali-phy/bali-phy.p/help.cc.o -c ../src/bali-phy/help.cc [165/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/system.cc.o -MF src/bali-phy/bali-phy.p/system.cc.o.d -o src/bali-phy/bali-phy.p/system.cc.o -c ../src/bali-phy/system.cc [166/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/paths.cc.o -MF src/bali-phy/bali-phy.p/paths.cc.o.d -o src/bali-phy/bali-phy.p/paths.cc.o -c ../src/bali-phy/paths.cc [167/297] c++ -Isrc/builtins/Array.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Array.so.p/Array.cc.o -MF src/builtins/Array.so.p/Array.cc.o.d -o src/builtins/Array.so.p/Array.cc.o -c ../src/builtins/Array.cc [168/297] c++ -o src/builtins/Array.so src/builtins/Array.so.p/Array.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Array.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [169/297] c++ -o src/builtins/Data.so src/builtins/Data.so.p/Data.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Data.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [170/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/cmd_line.cc.o -MF src/bali-phy/bali-phy.p/cmd_line.cc.o.d -o src/bali-phy/bali-phy.p/cmd_line.cc.o -c ../src/bali-phy/cmd_line.cc [171/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/A-T-model.cc.o -MF src/bali-phy/bali-phy.p/A-T-model.cc.o.d -o src/bali-phy/bali-phy.p/A-T-model.cc.o -c ../src/bali-phy/A-T-model.cc [172/297] c++ -Isrc/builtins/Prelude.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Prelude.so.p/Prelude.cc.o -MF src/builtins/Prelude.so.p/Prelude.cc.o.d -o src/builtins/Prelude.so.p/Prelude.cc.o -c ../src/builtins/Prelude.cc [173/297] c++ -o src/builtins/Prelude.so src/builtins/Prelude.so.p/Prelude.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Prelude.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [174/297] c++ -Isrc/bali-phy/bali-phy.p -Isrc/bali-phy -I../src/bali-phy -I. -I.. -Isrc -I../src -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-phy/bali-phy.p/loggers.cc.o -MF src/bali-phy/bali-phy.p/loggers.cc.o.d -o src/bali-phy/bali-phy.p/loggers.cc.o -c ../src/bali-phy/loggers.cc [175/297] c++ -Isrc/builtins/Pair.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Pair.so.p/Pair.cc.o -MF src/builtins/Pair.so.p/Pair.cc.o.d -o src/builtins/Pair.so.p/Pair.cc.o -c ../src/builtins/Pair.cc [176/297] c++ -o src/builtins/Pair.so src/builtins/Pair.so.p/Pair.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Pair.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [177/297] c++ -Isrc/builtins/Alphabet.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alphabet.so.p/Alphabet.cc.o -MF src/builtins/Alphabet.so.p/Alphabet.cc.o.d -o src/builtins/Alphabet.so.p/Alphabet.cc.o -c ../src/builtins/Alphabet.cc [178/297] c++ -Isrc/builtins/Modifiables.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Modifiables.so.p/Modifiables.cc.o -MF src/builtins/Modifiables.so.p/Modifiables.cc.o.d -o src/builtins/Modifiables.so.p/Modifiables.cc.o -c ../src/builtins/Modifiables.cc [179/297] c++ -o src/builtins/Alphabet.so src/builtins/Alphabet.so.p/Alphabet.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Alphabet.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [180/297] c++ -o src/builtins/Modifiables.so src/builtins/Modifiables.so.p/Modifiables.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Modifiables.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [181/297] c++ -o src/bali-phy/bali-phy src/bali-phy/bali-phy.p/link-partitions.cc.o src/bali-phy/bali-phy.p/bali-phy.cc.o src/bali-phy/bali-phy.p/help.cc.o src/bali-phy/bali-phy.p/A-T-model.cc.o src/bali-phy/bali-phy.p/files.cc.o src/bali-phy/bali-phy.p/loggers.cc.o src/bali-phy/bali-phy.p/system.cc.o src/bali-phy/bali-phy.p/cmd_line.cc.o src/bali-phy/bali-phy.p/paths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,-export-dynamic -Wl,--whole-archive -Wl,--start-group src/util/libutil.a src/libcommon.a src/computation/libcomputation.a src/libbaliphy.a -Wl,--no-whole-archive -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -ldl -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [182/297] c++ -Isrc/builtins/Range.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Range.so.p/Range.cc.o -MF src/builtins/Range.so.p/Range.cc.o.d -o src/builtins/Range.so.p/Range.cc.o -c ../src/builtins/Range.cc [183/297] c++ -o src/builtins/Range.so src/builtins/Range.so.p/Range.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Range.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [184/297] c++ -Isrc/builtins/Distribution.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Distribution.so.p/Distribution.cc.o -MF src/builtins/Distribution.so.p/Distribution.cc.o.d -o src/builtins/Distribution.so.p/Distribution.cc.o -c ../src/builtins/Distribution.cc [185/297] c++ -o src/builtins/Distribution.so src/builtins/Distribution.so.p/Distribution.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Distribution.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [186/297] c++ -Isrc/builtins/Alignment.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Alignment.so.p/Alignment.cc.o -MF src/builtins/Alignment.so.p/Alignment.cc.o.d -o src/builtins/Alignment.so.p/Alignment.cc.o -c ../src/builtins/Alignment.cc [187/297] c++ -o src/builtins/Alignment.so src/builtins/Alignment.so.p/Alignment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Alignment.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [188/297] c++ -Isrc/builtins/PopGen.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/PopGen.so.p/PopGen.cc.o -MF src/builtins/PopGen.so.p/PopGen.cc.o.d -o src/builtins/PopGen.so.p/PopGen.cc.o -c ../src/builtins/PopGen.cc [189/297] c++ -o src/builtins/PopGen.so src/builtins/PopGen.so.p/PopGen.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,PopGen.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [190/297] c++ -Isrc/builtins/Vector.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Vector.so.p/Vector.cc.o -MF src/builtins/Vector.so.p/Vector.cc.o.d -o src/builtins/Vector.so.p/Vector.cc.o -c ../src/builtins/Vector.cc [191/297] c++ -o src/builtins/Vector.so src/builtins/Vector.so.p/Vector.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Vector.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [192/297] c++ -Isrc/builtins/Environment.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Environment.so.p/Environment.cc.o -MF src/builtins/Environment.so.p/Environment.cc.o.d -o src/builtins/Environment.so.p/Environment.cc.o -c ../src/builtins/Environment.cc [193/297] c++ -o src/builtins/Environment.so src/builtins/Environment.so.p/Environment.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Environment.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [194/297] c++ -Isrc/builtins/MCMC.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/MCMC.so.p/MCMC.cc.o -MF src/builtins/MCMC.so.p/MCMC.cc.o.d -o src/builtins/MCMC.so.p/MCMC.cc.o -c ../src/builtins/MCMC.cc [195/297] c++ -o src/builtins/MCMC.so src/builtins/MCMC.so.p/MCMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,MCMC.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [196/297] c++ -Isrc/builtins/SModel.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/SModel.so.p/SModel.cc.o -MF src/builtins/SModel.so.p/SModel.cc.o.d -o src/builtins/SModel.so.p/SModel.cc.o -c ../src/builtins/SModel.cc [197/297] c++ -o src/builtins/SModel.so src/builtins/SModel.so.p/SModel.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,SModel.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [198/297] c++ -Isrc/builtins/Real.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Real.so.p/Real.cc.o -MF src/builtins/Real.so.p/Real.cc.o.d -o src/builtins/Real.so.p/Real.cc.o -c ../src/builtins/Real.cc [199/297] c++ -o src/builtins/Real.so src/builtins/Real.so.p/Real.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Real.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [200/297] c++ -Isrc/builtins/Bits.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Bits.so.p/Bits.cc.o -MF src/builtins/Bits.so.p/Bits.cc.o.d -o src/builtins/Bits.so.p/Bits.cc.o -c ../src/builtins/Bits.cc [201/297] c++ -Isrc/builtins/Text.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Text.so.p/Text.cc.o -MF src/builtins/Text.so.p/Text.cc.o.d -o src/builtins/Text.so.p/Text.cc.o -c ../src/builtins/Text.cc [202/297] c++ -o src/builtins/Text.so src/builtins/Text.so.p/Text.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Text.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [203/297] c++ -o src/builtins/Bits.so src/builtins/Bits.so.p/Bits.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Bits.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [204/297] c++ -Isrc/builtins/Char.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Char.so.p/Char.cc.o -MF src/builtins/Char.so.p/Char.cc.o.d -o src/builtins/Char.so.p/Char.cc.o -c ../src/builtins/Char.cc [205/297] c++ -o src/builtins/Char.so src/builtins/Char.so.p/Char.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Char.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [206/297] c++ -Isrc/builtins/Foreign.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/Foreign.so.p/Foreign.cc.o -MF src/builtins/Foreign.so.p/Foreign.cc.o.d -o src/builtins/Foreign.so.p/Foreign.cc.o -c ../src/builtins/Foreign.cc [207/297] c++ -o src/builtins/Foreign.so src/builtins/Foreign.so.p/Foreign.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,Foreign.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [208/297] c++ -Isrc/model_P.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/model_P.p/tools_model_P.cc.o -MF src/model_P.p/tools_model_P.cc.o.d -o src/model_P.p/tools_model_P.cc.o -c ../src/tools/model_P.cc [209/297] c++ -o src/model_P src/model_P.p/tools_model_P.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [210/297] c++ -Isrc/stats-select.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/stats-select.p/tools_stats-select.cc.o -MF src/stats-select.p/tools_stats-select.cc.o.d -o src/stats-select.p/tools_stats-select.cc.o -c ../src/tools/stats-select.cc [211/297] c++ -o src/stats-select src/stats-select.p/tools_stats-select.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [212/297] c++ -Isrc/statreport.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/statreport.p/tools_statreport.cc.o -MF src/statreport.p/tools_statreport.cc.o.d -o src/statreport.p/tools_statreport.cc.o -c ../src/tools/statreport.cc [213/297] c++ -Isrc/builtins/SMC.so.p -Isrc/builtins -I../src/builtins -I../src/util/include -I. -I.. -Isrc -I../src -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -isystem/usr/include/eigen3 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/builtins/SMC.so.p/SMC.cc.o -MF src/builtins/SMC.so.p/SMC.cc.o.d -o src/builtins/SMC.so.p/SMC.cc.o -c ../src/builtins/SMC.cc [214/297] c++ -o src/builtins/SMC.so src/builtins/SMC.so.p/SMC.cc.o -Wl,--as-needed -Wl,--allow-shlib-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,SMC.so -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -Wl,--end-group [215/297] c++ -o src/statreport src/statreport.p/tools_statreport.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [216/297] c++ -Isrc/alignment-gild.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-gild.p/tools_alignment-gild.cc.o -MF src/alignment-gild.p/tools_alignment-gild.cc.o.d -o src/alignment-gild.p/tools_alignment-gild.cc.o -c ../src/tools/alignment-gild.cc [217/297] c++ -o src/alignment-gild src/alignment-gild.p/tools_alignment-gild.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [218/297] c++ -Isrc/alignment-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-consensus.p/tools_alignment-consensus.cc.o -MF src/alignment-consensus.p/tools_alignment-consensus.cc.o.d -o src/alignment-consensus.p/tools_alignment-consensus.cc.o -c ../src/tools/alignment-consensus.cc [219/297] c++ -o src/alignment-consensus src/alignment-consensus.p/tools_alignment-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [220/297] c++ -Isrc/alignment-chop-internal.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -MF src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o.d -o src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -c ../src/tools/alignment-chop-internal.cc [221/297] c++ -o src/alignment-chop-internal src/alignment-chop-internal.p/tools_alignment-chop-internal.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [222/297] c++ -Isrc/alignment-max.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-max.p/tools_alignment-max.cc.o -MF src/alignment-max.p/tools_alignment-max.cc.o.d -o src/alignment-max.p/tools_alignment-max.cc.o -c ../src/tools/alignment-max.cc [223/297] c++ -o src/alignment-max src/alignment-max.p/tools_alignment-max.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [224/297] c++ -Isrc/alignment-info.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-info.p/tools_alignment-info.cc.o -MF src/alignment-info.p/tools_alignment-info.cc.o.d -o src/alignment-info.p/tools_alignment-info.cc.o -c ../src/tools/alignment-info.cc [225/297] c++ -o src/alignment-info src/alignment-info.p/tools_alignment-info.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [226/297] c++ -Isrc/alignment-indices.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-indices.p/tools_alignment-indices.cc.o -MF src/alignment-indices.p/tools_alignment-indices.cc.o.d -o src/alignment-indices.p/tools_alignment-indices.cc.o -c ../src/tools/alignment-indices.cc [227/297] c++ -o src/alignment-indices src/alignment-indices.p/tools_alignment-indices.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [228/297] c++ -Isrc/alignment-translate.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-translate.p/tools_alignment-translate.cc.o -MF src/alignment-translate.p/tools_alignment-translate.cc.o.d -o src/alignment-translate.p/tools_alignment-translate.cc.o -c ../src/tools/alignment-translate.cc [229/297] c++ -o src/alignment-translate src/alignment-translate.p/tools_alignment-translate.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [230/297] c++ -Isrc/alignment-find.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-find.p/tools_alignment-find.cc.o -MF src/alignment-find.p/tools_alignment-find.cc.o.d -o src/alignment-find.p/tools_alignment-find.cc.o -c ../src/tools/alignment-find.cc [231/297] c++ -o src/alignment-find src/alignment-find.p/tools_alignment-find.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [232/297] c++ -Isrc/alignment-cat.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-cat.p/tools_alignment-cat.cc.o -MF src/alignment-cat.p/tools_alignment-cat.cc.o.d -o src/alignment-cat.p/tools_alignment-cat.cc.o -c ../src/tools/alignment-cat.cc [233/297] c++ -o src/alignment-cat src/alignment-cat.p/tools_alignment-cat.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [234/297] c++ -Isrc/tree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -MF src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o.d -o src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -c ../src/tools/tree-mean-lengths.cc [235/297] c++ -o src/tree-mean-lengths src/tree-mean-lengths.p/tools_tree-mean-lengths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [236/297] c++ -Isrc/mctree-mean-lengths.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -MF src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o.d -o src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -c ../src/tools/mctree-mean-lengths.cc [237/297] c++ -o src/mctree-mean-lengths src/mctree-mean-lengths.p/tools_mctree-mean-lengths.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [238/297] c++ -Isrc/trees-consensus.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-consensus.p/tools_trees-consensus.cc.o -MF src/trees-consensus.p/tools_trees-consensus.cc.o.d -o src/trees-consensus.p/tools_trees-consensus.cc.o -c ../src/tools/trees-consensus.cc [239/297] c++ -Isrc/trees-to-SRQ.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -MF src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o.d -o src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -c ../src/tools/trees-to-SRQ.cc [240/297] c++ -o src/trees-to-SRQ src/trees-to-SRQ.p/tools_trees-to-SRQ.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [241/297] c++ -o src/trees-consensus src/trees-consensus.p/tools_trees-consensus.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [242/297] c++ -Isrc/pickout.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/pickout.p/tools_pickout.cc.o -MF src/pickout.p/tools_pickout.cc.o.d -o src/pickout.p/tools_pickout.cc.o -c ../src/tools/pickout.cc [243/297] c++ -o src/pickout src/pickout.p/tools_pickout.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [244/297] c++ -Isrc/cut-range.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/cut-range.p/tools_cut-range.cc.o -MF src/cut-range.p/tools_cut-range.cc.o.d -o src/cut-range.p/tools_cut-range.cc.o -c ../src/tools/cut-range.cc [245/297] c++ -o src/cut-range src/cut-range.p/tools_cut-range.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [246/297] c++ -Isrc/trees-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-distances.p/tools_trees-distances.cc.o -MF src/trees-distances.p/tools_trees-distances.cc.o.d -o src/trees-distances.p/tools_trees-distances.cc.o -c ../src/tools/trees-distances.cc [247/297] c++ -o src/trees-distances src/trees-distances.p/tools_trees-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [248/297] c++ -Isrc/tree-tool.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/tree-tool.p/tools_tree-tool.cc.o -MF src/tree-tool.p/tools_tree-tool.cc.o.d -o src/tree-tool.p/tools_tree-tool.cc.o -c ../src/tools/tree-tool.cc [249/297] c++ -o src/tree-tool src/tree-tool.p/tools_tree-tool.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [250/297] c++ -Isrc/alignments-diff.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignments-diff.p/tools_alignments-diff.cc.o -MF src/alignments-diff.p/tools_alignments-diff.cc.o.d -o src/alignments-diff.p/tools_alignments-diff.cc.o -c ../src/tools/alignments-diff.cc [251/297] c++ -o src/alignments-diff src/alignments-diff.p/tools_alignments-diff.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [252/297] c++ -Isrc/alignment-thin.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-thin.p/tools_alignment-thin.cc.o -MF src/alignment-thin.p/tools_alignment-thin.cc.o.d -o src/alignment-thin.p/tools_alignment-thin.cc.o -c ../src/tools/alignment-thin.cc [253/297] c++ -o src/alignment-thin src/alignment-thin.p/tools_alignment-thin.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [254/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_colors.cc.o -MF src/alignment-draw.p/tools_colors.cc.o.d -o src/alignment-draw.p/tools_colors.cc.o -c ../src/tools/colors.cc [255/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_bootstrap.cc.o -MF src/trees-bootstrap.p/tools_bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_bootstrap.cc.o -c ../src/tools/bootstrap.cc [256/297] c++ -Isrc/alignment-draw.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-draw.p/tools_alignment-draw.cc.o -MF src/alignment-draw.p/tools_alignment-draw.cc.o.d -o src/alignment-draw.p/tools_alignment-draw.cc.o -c ../src/tools/alignment-draw.cc [257/297] c++ -o src/alignment-draw src/alignment-draw.p/tools_alignment-draw.cc.o src/alignment-draw.p/tools_colors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [258/297] c++ -Isrc/trees-bootstrap.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -MF src/trees-bootstrap.p/tools_trees-bootstrap.cc.o.d -o src/trees-bootstrap.p/tools_trees-bootstrap.cc.o -c ../src/tools/trees-bootstrap.cc [259/297] c++ -o src/trees-bootstrap src/trees-bootstrap.p/tools_trees-bootstrap.cc.o src/trees-bootstrap.p/tools_bootstrap.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [260/297] c++ -Isrc/alignment-distances.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/alignment-distances.p/tools_alignment-distances.cc.o -MF src/alignment-distances.p/tools_alignment-distances.cc.o.d -o src/alignment-distances.p/tools_alignment-distances.cc.o -c ../src/tools/alignment-distances.cc [261/297] c++ -o src/alignment-distances src/alignment-distances.p/tools_alignment-distances.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [262/297] c++ -Isrc/extract-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/extract-ancestors.p/tools_extract-ancestors.cc.o -MF src/extract-ancestors.p/tools_extract-ancestors.cc.o.d -o src/extract-ancestors.p/tools_extract-ancestors.cc.o -c ../src/tools/extract-ancestors.cc [263/297] c++ -o src/extract-ancestors src/extract-ancestors.p/tools_extract-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [264/297] c++ -Isrc/bali-subsample.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/bali-subsample.p/tools_subsample.cc.o -MF src/bali-subsample.p/tools_subsample.cc.o.d -o src/bali-subsample.p/tools_subsample.cc.o -c ../src/tools/subsample.cc [265/297] c++ -o src/bali-subsample src/bali-subsample.p/tools_subsample.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [266/297] /usr/bin/meson --internal exe --capture doc/model_P.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/model_P.md [267/297] /usr/bin/meson --internal exe --capture doc/bali-phy.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bali-phy.md [268/297] /usr/bin/meson --internal exe --capture doc/statreport.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/statreport.md [269/297] /usr/bin/meson --internal exe --capture doc/stats-select.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/stats-select.md [270/297] c++ -Isrc/draw-tree.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/draw-tree.p/tools_draw-tree.cc.o -MF src/draw-tree.p/tools_draw-tree.cc.o.d -o src/draw-tree.p/tools_draw-tree.cc.o -c ../src/tools/draw-tree.cc ../src/tools/draw-tree.cc: In function ‘MC_tree_with_lengths collapse_MC_tree(const MC_tree_with_lengths&)’: ../src/tools/draw-tree.cc:3351:10: warning: unused variable ‘right1’ [-Wunused-variable] 3351 | int right1 = MC1.mapping[b1]; | ^~~~~~ [271/297] /usr/bin/meson --internal exe --capture doc/alignment-gild.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-gild.md [272/297] /usr/bin/meson --internal exe --capture doc/alignment-consensus.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-consensus.md [273/297] /usr/bin/meson --internal exe --capture doc/alignment-max.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-max.md [274/297] /usr/bin/meson --internal exe --capture doc/alignment-chop-internal.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-chop-internal.md [275/297] c++ -o src/draw-tree src/draw-tree.p/tools_draw-tree.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm /usr/lib/x86_64-linux-gnu/libcairo.so -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX [276/297] /usr/bin/meson --internal exe --capture doc/alignment-indices.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-indices.md [277/297] /usr/bin/meson --internal exe --capture doc/alignment-info.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-info.md [278/297] /usr/bin/meson --internal exe --capture doc/alignment-cat.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-cat.md [279/297] /usr/bin/meson --internal exe --capture doc/alignment-translate.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-translate.md [280/297] /usr/bin/meson --internal exe --capture doc/alignment-find.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-find.md [281/297] /usr/bin/meson --internal exe --capture doc/trees-consensus.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/trees-consensus.md [282/297] /usr/bin/meson --internal exe --capture doc/tree-mean-lengths.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/tree-mean-lengths.md [283/297] /usr/bin/meson --internal exe --capture doc/trees-to-SRQ.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/trees-to-SRQ.md [284/297] /usr/bin/meson --internal exe --capture doc/mctree-mean-lengths.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/mctree-mean-lengths.md [285/297] /usr/bin/meson --internal exe --capture doc/alignments-diff.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignments-diff.md [286/297] /usr/bin/meson --internal exe --capture doc/alignment-distances.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-distances.md [287/297] /usr/bin/meson --internal exe --capture doc/tree-tool.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/tree-tool.md [288/297] /usr/bin/meson --internal exe --capture doc/alignment-draw.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/alignment-draw.md [289/297] /usr/bin/meson --internal exe --capture doc/draw-tree.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/draw-tree.md [290/297] /usr/bin/meson --internal exe --capture doc/trees-bootstrap.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/trees-bootstrap.md [291/297] /usr/bin/meson --internal exe --capture doc/extract-ancestors.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/extract-ancestors.md [292/297] /usr/bin/meson --internal exe --capture doc/summarize-ancestors.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/summarize-ancestors.md [293/297] /usr/bin/meson --internal exe --capture doc/bali-subsample.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bali-subsample.md [294/297] /usr/bin/meson --internal exe --capture doc/bp-analyze.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bp-analyze.md [295/297] /usr/bin/meson --internal exe --capture doc/bali-phy-pkg.1 -- /usr/bin/pandoc -s -t man -f markdown-smart ../doc/man/bali-phy-pkg.md [296/297] c++ -Isrc/summarize-ancestors.p -Isrc -I../src -I. -I.. -I../src/util/include -I/usr/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -O3 -DHAVE_CONFIG_H -Wno-sign-compare -Wno-maybe-uninitialized -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -fdiagnostics-show-template-tree -DNDEBUG -DNDEBUG_DP -funroll-loops -fno-math-errno -fno-signed-zeros -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_FILESYSTEM_DYN_LINK=1 -DBOOST_CHRONO_DYN_LINK=1 -DBOOST_RANDOM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK=1 -DBOOST_ALL_NO_LIB -MD -MQ src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -MF src/summarize-ancestors.p/tools_summarize-ancestors.cc.o.d -o src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -c ../src/tools/summarize-ancestors.cc [297/297] c++ -o src/summarize-ancestors src/summarize-ancestors.p/tools_summarize-ancestors.cc.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/util/libutil.a src/libcommon.a /usr/lib/x86_64-linux-gnu/libboost_random.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 -lm -Wl,--end-group -Wl,-rpath,XXXXXXXXXXXXXXXXXXXXXXXX dh_auto_test -a -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 meson test ninja: Entering directory `/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu' [1/4] Generating git-version.h with a custom command 1/36 bali-phy version OK 0.16s 2/36 bali-phy help OK 0.10s 4/36 bali-phy 5d +A 50 OK 75.53s 5/36 bali-phy 48 +A 3 OK 99.13s 6/36 bali-phy 5d -A 200 OK 65.58s 7/36 model_P --help OK 0.13s 8/36 statreport --help OK 0.02s 9/36 stats-select --help OK 0.09s 10/36 alignment-gild --help OK 0.09s 11/36 alignment-consensus --help OK 0.09s 12/36 alignment-max --help OK 0.09s 13/36 alignment-chop-internal --help OK 0.11s 14/36 alignment-indices --help OK 0.08s 15/36 alignment-info --help OK 0.11s 16/36 alignment-cat --help OK 0.10s 17/36 alignment-translate --help OK 0.10s 18/36 alignment-find --help OK 0.09s 19/36 trees-consensus --help OK 0.09s 20/36 tree-mean-lengths --help OK 0.10s 21/36 mctree-mean-lengths --help OK 0.02s 22/36 trees-to-SRQ --help OK 0.09s 23/36 pickout --help OK 0.10s 24/36 cut-range --help OK 0.22s 25/36 trees-distances --help OK 0.09s 26/36 alignment-thin --help OK 0.10s 27/36 alignments-diff --help OK 0.10s 28/36 tree-tool --help OK 0.10s 29/36 alignment-distances --help OK 0.01s 30/36 alignment-draw --help OK 0.02s 31/36 trees-bootstrap --help OK 0.10s 32/36 draw-tree --help OK 0.21s 33/36 extract-ancestors --help OK 0.07s 34/36 summarize-ancestors --help OK 0.09s 35/36 subsample --help OK 0.01s 36/36 bali-phy testsuite OK 517.90s Summary of Failures: 3/36 bali-phy 5d test TIMEOUT 30.25s Ok: 35 Expected Fail: 0 Fail: 0 Unexpected Pass: 0 Skipped: 0 Timeout: 1 Full log written to /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/meson-logs/testlog.txt cd obj-x86_64-linux-gnu && tail -v -n \+0 meson-logs/testlog.txt ==> meson-logs/testlog.txt <== Log of Meson test suite run on 2021-10-11T23:24:20.690603 Inherited environment: DEB_HOST_MULTIARCH='x86_64-linux-gnu' LC_ALL='C.UTF-8' DEB_HOST_GNU_SYSTEM='linux-gnu' DEB_BUILD_GNU_TYPE='x86_64-linux-gnu' DEB_TARGET_ARCH_LIBC='gnu' DEB_BUILD_ARCH_ENDIAN='little' DEB_BUILD_GNU_SYSTEM='linux-gnu' DEB_BUILD_ARCH_BITS='64' DEB_BUILD_OPTIONS='parallel=4' DEB_CXXFLAGS_MAINT_APPEND='-O3' DEB_HOST_ARCH='amd64' DEB_TARGET_ARCH_ENDIAN='little' PWD='/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg' SOURCE_DATE_EPOCH='1612666578' MMDEBSTRAP_APT_CONFIG='/tmp/mmdebstrap.w0hk_H1ON8/tmp/mmdebstrap.apt.conf.MhA3_Kr5Q9vp' OLDPWD='/' DEB_HOST_ARCH_BITS='64' LANG='C.UTF-8' MAKEFLAGS='' MMDEBSTRAP_HOOKSOCK='6' DEB_TARGET_ARCH='amd64' MMDEBSTRAP_MODE='root' DEB_HOST_GNU_CPU='x86_64' DEB_BUILD_ARCH_LIBC='gnu' MFLAGS='' DEB_TARGET_ARCH_BITS='64' DEBCONF_NONINTERACTIVE_SEEN='true' DEB_BUILD_ARCH_CPU='amd64' DEB_HOST_ARCH_OS='linux' SHELL='/bin/bash' SHLVL='0' DEB_HOST_ARCH_CPU='amd64' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin' DEB_BUILD_ARCH_ABI='base' LANGUAGE='C.UTF-8' DEB_BUILD_ARCH='amd64' DEB_HOST_ARCH_LIBC='gnu' DEB_TARGET_ARCH_CPU='amd64' DEB_HOST_GNU_TYPE='x86_64-linux-gnu' DEB_BUILD_ARCH_OS='linux' LOGNAME='builduser' DEB_TARGET_MULTIARCH='x86_64-linux-gnu' DEB_BUILD_GNU_CPU='x86_64' DEB_TARGET_ARCH_OS='linux' USER='builduser' DEB_HOST_ARCH_ABI='base' DEB_BUILD_MULTIARCH='x86_64-linux-gnu' MMDEBSTRAP_HOOK='customize' DEB_TARGET_GNU_TYPE='x86_64-linux-gnu' DEB_TARGET_ARCH_ABI='base' _='/usr/bin/env' DEB_TARGET_GNU_CPU='x86_64' DEBIAN_FRONTEND='noninteractive' HOME='/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/debian/.debhelper/generated/_source/home' DEB_RULES_REQUIRES_ROOT='no' DEB_TARGET_GNU_SYSTEM='linux-gnu' DEB_HOST_ARCH_ENDIAN='little' DEB_BUILD_MAINT_OPTIONS='hardening=+all' DEB_CFLAGS_MAINT_APPEND='-O3' MAKELEVEL='1' DH_INTERNAL_BUILDFLAGS='1' CFLAGS='-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3' CPPFLAGS='-Wdate-time -D_FORTIFY_SOURCE=2' CXXFLAGS='-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3' DFLAGS='-frelease' FCFLAGS='-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong' FFLAGS='-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong' GCJFLAGS='-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong' LDFLAGS='-Wl,-z,relro -Wl,-z,now' OBJCFLAGS='-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' OBJCXXFLAGS='-g -O2 -ffile-prefix-map=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' XDG_RUNTIME_DIR='/tmp/dh-xdg-rundir-0H01ZVrI' MESON_TESTTHREADS='4' 1/36 bali-phy version OK 0.16s --- command --- 23:24:20 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --version --- stdout --- VERSION: 3.6.0 BUILD: Feb 7 2021 02:56:18 ARCH: linux x86_64 COMPILER: gcc 10.2.1 x86_64 ------- 2/36 bali-phy help OK 0.10s --- command --- 23:24:20 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --help --- stdout --- Bayesian Inference of Alignment and Phylogeny Usage: bali-phy [ ...] [OPTIONS] Basic options: General options: -h [ --help ] [=arg(=basic)] Print usage information. -v [ --version ] Print version information. -t [ --test ] Analyze the initial values and exit. -c [ --config ] arg Command file to read. MCMC options: -i [ --iterations ] arg The number of iterations to run. -n [ --name ] arg Name for the output directory to create. Parameter options: --align arg Sequence file & initial alignment. -T [ --tree ] arg File with initial tree Model options: -A [ --alphabet ] arg The alphabet. -S [ --smodel ] arg Substitution model. -I [ --imodel ] arg Insertion-deletion model. -R [ --scale ] arg Prior on the scale. -L [ --link ] arg Link partitions. Showing basic command line options. Not all options are shown! * See `bali-phy help advanced` to see more options. See `bali-phy help option` for help on option. For example, * `bali-phy help alphabet` shows help on the --alphabet command. * `bali-phy help normal` shows help on the normal distribution. * `bali-phy help tn93` shows help on the TN93 model. * `bali-phy help log` shows help on the log function. To see help on one of the following topics, run `bali-phy help topic` ------- 3/36 bali-phy 5d test TIMEOUT 30.25s --- command --- 23:24:20 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --test --package-path=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg --- stdout --- T:topology ~ uniform on tree topologies T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] Partition P1: file = /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta alphabet = DNA subst = tn93 (S1) indel = rs07 (I1) scale ~ gamma[0.5,2] (Scale1) Substitution model S1 priors: tn93:kappaPur ~ log_normal[log[2],0.25] tn93:kappaPyr ~ log_normal[log[2],0.25] tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] Insertion/deletion model I1 priors: rs07:log_rate ~ laplace[-4,0.707] rs07:mean_length ~ shifted_exponential[10,1] iter = 0 prior = -47.664688044554239 likelihood = -1166.404007897333486 posterior = -1214.068695941887654 prior_A = -33.719204684381523 |A| = 126 #indels = 4 |indels| = 9 #substs = 252 P1/likelihood = -1166.404007897333486 P1/prior_A = -33.719204684381523 P1/|A| = 126 P1/#indels = 4 P1/|indels| = 9 P1/#substs = 252 Scale[1]*|T| = 1.339593153123361 |T| = 1.928919149656538 rs07:log_rate = -4.745996138208587 rs07:mean_length = 22.327126604980595 tn93:kappaPur = 3.300106069473431 tn93:kappaPyr = 2.2451165021283908 tn93:pi[A] = 0.5154195301415474 tn93:pi[C] = 0.1850615762463695 tn93:pi[G] = 0.18058378426345734 tn93:pi[T] = 0.11893510934862575 scale[1] = 0.6944786427994604 scale1 = 0.6944786427994604 start time: Mon Oct 11 23:24:20 2021 end time: Mon Oct 11 23:24:50 2021 total (elapsed) time: 29 seconds total (CPU) time: 5 seconds ------- 4/36 bali-phy 5d +A 50 OK 75.53s --- command --- 23:24:20 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --iter=50 --package-path=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg --- stdout --- T:topology ~ uniform on tree topologies T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] Partition P1: file = /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta alphabet = DNA subst = tn93 (S1) indel = rs07 (I1) scale ~ gamma[0.5,2] (Scale1) Substitution model S1 priors: tn93:kappaPur ~ log_normal[log[2],0.25] tn93:kappaPyr ~ log_normal[log[2],0.25] tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] Insertion/deletion model I1 priors: rs07:log_rate ~ laplace[-4,0.707] rs07:mean_length ~ shifted_exponential[10,1] Beginning pre-burnin: 3 iterations. Start #1 prior = -42.6426 likelihood = -1799.62 |T| = 1.40053 Scale1*|T| = 0.189979 Tree (S)ize #1 prior = -22.9948 likelihood = -1443.24 |T| = 1.9256 Scale1*|T| = 43.2659 Tree (S)ize #2 prior = -25.2409 likelihood = -1439.21 |T| = 4.10932 Scale1*|T| = 30.6972 Tree (S)ize #3 prior = -25.4693 likelihood = -1439.37 |T| = 4.10932 Scale1*|T| = 32.3578 (S)+Branch (L)engths #1 prior = -11.8428 likelihood = -1392.08 |T| = 1.26718 Scale1*|T| = 8.52831 (S)+Branch (L)engths #2 prior = -2.87669 likelihood = -1311.19 |T| = 0.464879 Scale1*|T| = 2.14354 (S)+Branch (L)engths #3 prior = -7.65594 likelihood = -1236.95 |T| = 0.813804 Scale1*|T| = 2.11858 (S)+(L)+(P)arameters #1 prior = -36.8281 likelihood = -840.765 |T| = 1.84779 Scale1*|T| = 3.89181 (S)+(L)+(P)arameters #2 prior = -46.6366 likelihood = -808.416 |T| = 1.73255 Scale1*|T| = 5.24172 (S)+(L)+(P)arameters #3 prior = -47.536 likelihood = -801.907 |T| = 1.57169 Scale1*|T| = 8.00352 (S)+(L)+(P)+NNI #1 prior = -51.9431 likelihood = -801.07 |T| = 2.46235 Scale1*|T| = 7.22271 (S)+(L)+(P)+NNI #2 prior = -42.7897 likelihood = -798.872 |T| = 0.754745 Scale1*|T| = 6.78962 (S)+(L)+(P)+NNI #3 prior = -48.4652 likelihood = -795.453 |T| = 1.70759 Scale1*|T| = 7.43591 (S)+(L)+(P)+NNI #4 prior = -48.8226 likelihood = -794.677 |T| = 1.55652 Scale1*|T| = 8.88369 SPR #1 prior = -55.6528 likelihood = -792.289 |T| = 3.82873 Scale1*|T| = 13.3308 (S)+(L)+(P)+NNI #1 prior = -42.2617 likelihood = -791.393 |T| = 1.18447 Scale1*|T| = 10.1913 (S)+(L)+(P)+NNI #2 prior = -41.0506 likelihood = -791.997 |T| = 1.36364 Scale1*|T| = 9.943 (S)+(L)+(P)+NNI #3 prior = -41.789 likelihood = -792.006 |T| = 0.768949 Scale1*|T| = 9.17022 Finished pre-burnin in 0.24 seconds. BAli-Phy does NOT detect how many iterations is sufficient: You need to monitor convergence and kill it when done. Maximum number of iterations set to 50. Beginning MCMC computations. - Future screen output sent to '5d-1/C1.out' - Future debugging output sent to '5d-1/C1.err' - Sampled trees logged to '5d-1/C1.trees' - Sampled alignments logged to '5d-1/C1.P.fastas' - Run info written to '5d-1/C1.run.json' - Sampled numerical parameters logged to '5d-1/C1.log' as TSV You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). See the manual at http://www.bali-phy.org/README.xhtml for further information. --- stderr --- Created directory '5d-1/' for output files. ------- 5/36 bali-phy 48 +A 3 OK 99.13s --- command --- 23:24:20 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/48-muscle.fasta --iter=3 --package-path=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg --- stdout --- T:topology ~ uniform on tree topologies T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] Partition P1: file = /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/48-muscle.fasta alphabet = RNA subst = tn93 (S1) indel = rs07 (I1) scale ~ gamma[0.5,2] (Scale1) Substitution model S1 priors: tn93:kappaPur ~ log_normal[log[2],0.25] tn93:kappaPyr ~ log_normal[log[2],0.25] tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] Insertion/deletion model I1 priors: rs07:log_rate ~ laplace[-4,0.707] rs07:mean_length ~ shifted_exponential[10,1] Beginning pre-burnin: 3 iterations. Start #1 prior = -2350.22 likelihood = -11566.3 |T| = 0.890762 Scale1*|T| = 0.570256 Tree (S)ize #1 prior = 159.5 likelihood = -7091.16 |T| = 0.890762 Scale1*|T| = 23.4484 Tree (S)ize #2 prior = 145.564 likelihood = -7082.61 |T| = 1.04363 Scale1*|T| = 26.3931 Tree (S)ize #3 prior = 118.546 likelihood = -7082.63 |T| = 1.4023 Scale1*|T| = 26.3542 (S)+Branch (L)engths #1 prior = 37.4602 likelihood = -6256.61 |T| = 2.7626 Scale1*|T| = 29.6734 (S)+Branch (L)engths #2 prior = 103.792 likelihood = -6047.96 |T| = 1.63814 Scale1*|T| = 21.8538 (S)+Branch (L)engths #3 prior = 99.2939 likelihood = -5992.55 |T| = 1.77223 Scale1*|T| = 22.9598 (S)+(L)+(P)arameters #1 prior = 118.365 likelihood = -5838.37 |T| = 1.47621 Scale1*|T| = 22.4828 (S)+(L)+(P)arameters #2 prior = 146.047 likelihood = -5766.24 |T| = 1.09963 Scale1*|T| = 21.0977 (S)+(L)+(P)arameters #3 prior = 142.148 likelihood = -5737.14 |T| = 1.10569 Scale1*|T| = 19.7379 (S)+(L)+(P)+NNI #1 prior = 140.962 likelihood = -5626.16 |T| = 0.974742 Scale1*|T| = 18.6189 (S)+(L)+(P)+NNI #2 prior = 104.667 likelihood = -5406.22 |T| = 1.43123 Scale1*|T| = 16.6684 (S)+(L)+(P)+NNI #3 prior = 157.711 likelihood = -5231.61 |T| = 0.863585 Scale1*|T| = 14.1925 (S)+(L)+(P)+NNI #4 prior = 122.404 likelihood = -5085.82 |T| = 1.27573 Scale1*|T| = 14.9248 (S)+(L)+(P)+NNI #5 prior = 164.421 likelihood = -5042.7 |T| = 0.80536 Scale1*|T| = 14.5358 (S)+(L)+(P)+NNI #6 prior = 123.573 likelihood = -5002.89 |T| = 1.32275 Scale1*|T| = 14.6508 SPR #1 prior = 129.464 likelihood = -4521.34 |T| = 1.11932 Scale1*|T| = 12.1824 (S)+(L)+(P)+NNI #1 prior = 127.945 likelihood = -4516.27 |T| = 1.14507 Scale1*|T| = 11.1591 (S)+(L)+(P)+NNI #2 prior = 137.185 likelihood = -4510.85 |T| = 0.991252 Scale1*|T| = 11.0451 (S)+(L)+(P)+NNI #3 prior = 108.511 likelihood = -4505.46 |T| = 1.42178 Scale1*|T| = 11.2063 Finished pre-burnin in 6.75 seconds. BAli-Phy does NOT detect how many iterations is sufficient: You need to monitor convergence and kill it when done. Maximum number of iterations set to 3. Beginning MCMC computations. - Future screen output sent to '48-muscle-1/C1.out' - Future debugging output sent to '48-muscle-1/C1.err' - Sampled trees logged to '48-muscle-1/C1.trees' - Sampled alignments logged to '48-muscle-1/C1.P.fastas' - Run info written to '48-muscle-1/C1.run.json' - Sampled numerical parameters logged to '48-muscle-1/C1.log' as TSV You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). See the manual at http://www.bali-phy.org/README.xhtml for further information. --- stderr --- Created directory '48-muscle-1/' for output files. ------- 6/36 bali-phy 5d -A 200 OK 65.58s --- command --- 23:24:20 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta --iter=200 --package-path=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg -Inone --- stdout --- T:topology ~ uniform on tree topologies T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] Partition P1: file = /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/../examples/sequences/5S-rRNA/5d.fasta alphabet = DNA subst = tn93 (S1) indel = none scale ~ gamma[0.5,2] (Scale1) Substitution model S1 priors: tn93:kappaPur ~ log_normal[log[2],0.25] tn93:kappaPyr ~ log_normal[log[2],0.25] tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] Beginning pre-burnin: 3 iterations. Start #1 prior = 2.87301 likelihood = -2421.93 |T| = 0.38855 Scale1*|T| = 0.00614327 Tree (S)ize #1 prior = -5.93857 likelihood = -1400.12 |T| = 0.535808 Scale1*|T| = 4.34947 Tree (S)ize #2 prior = -3.32937 likelihood = -1278.99 |T| = 0.649399 Scale1*|T| = 1.36825 Tree (S)ize #3 prior = -2.92923 likelihood = -1279.18 |T| = 0.592417 Scale1*|T| = 1.34637 (S)+Branch (L)engths #1 prior = -0.631495 likelihood = -1218.91 |T| = 0.670824 Scale1*|T| = 1.54502 (S)+Branch (L)engths #2 prior = -0.465502 likelihood = -1199.3 |T| = 0.522519 Scale1*|T| = 1.17625 (S)+Branch (L)engths #3 prior = -5.67134 likelihood = -1197.29 |T| = 0.773584 Scale1*|T| = 1.24764 (S)+(L)+(P)arameters #1 prior = -15.6335 likelihood = -1083.62 |T| = 0.784456 Scale1*|T| = 1.99767 (S)+(L)+(P)arameters #2 prior = -19.0692 likelihood = -859.805 |T| = 1.01073 Scale1*|T| = 8.60197 (S)+(L)+(P)arameters #3 prior = -12.6371 likelihood = -798.368 |T| = 2.17163 Scale1*|T| = 4.70123 (S)+(L)+(P)+NNI #1 prior = -16.2479 likelihood = -793.71 |T| = 3.0289 Scale1*|T| = 7.30859 (S)+(L)+(P)+NNI #2 prior = -7.72584 likelihood = -792.442 |T| = 0.961044 Scale1*|T| = 6.7194 (S)+(L)+(P)+NNI #3 prior = -13.219 likelihood = -791.877 |T| = 2.15768 Scale1*|T| = 9.38366 (S)+(L)+(P)+NNI #4 prior = -8.54383 likelihood = -795.979 |T| = 0.922208 Scale1*|T| = 7.84231 SPR #1 prior = -9.50648 likelihood = -795.353 |T| = 1.07913 Scale1*|T| = 9.11983 (S)+(L)+(P)+NNI #1 prior = -10.8648 likelihood = -794.274 |T| = 1.45228 Scale1*|T| = 8.77716 (S)+(L)+(P)+NNI #2 prior = -16.944 likelihood = -794.938 |T| = 1.86359 Scale1*|T| = 5.48886 (S)+(L)+(P)+NNI #3 prior = -19.9162 likelihood = -793.462 |T| = 2.91819 Scale1*|T| = 6.3157 Finished pre-burnin in 0.26 seconds. BAli-Phy does NOT detect how many iterations is sufficient: You need to monitor convergence and kill it when done. Maximum number of iterations set to 200. Beginning MCMC computations. - Future screen output sent to '5d-2/C1.out' - Future debugging output sent to '5d-2/C1.err' - Sampled trees logged to '5d-2/C1.trees' - Sampled alignments logged to '5d-2/C1.P.fastas' - Run info written to '5d-2/C1.run.json' - Sampled numerical parameters logged to '5d-2/C1.log' as TSV You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). See the manual at http://www.bali-phy.org/README.xhtml for further information. --- stderr --- Created directory '5d-2/' for output files. Partition #1: 126 columns -> 110 unique patterns. ------- 7/36 model_P --help OK 0.13s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/model_P --help --- stdout --- Compute marginal likelihoods using stabilized harmonic mean estimator Usage: model_P < in-file Allowed options: -h [ --help ] produce help message --seed arg random seed --verbose Output more log messages on stderr. ------- 8/36 statreport --help OK 0.02s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/statreport --help --- stdout --- Compute summary statistics for tab-delimited data files. Usage: statreport [OPTIONS] file1 [file2 file3 ... ] All options: -h [ --help ] Produce help message. -V [ --verbose ] Output more log messages on stderr. -s [ --skip ] arg (=10%) Number of initial lines to skip. -x [ --subsample ] arg (=1) Factor by which to sub-sample. -u [ --until ] arg Read up to this iteration. -I [ --ignore ] arg Do not analyze these fields. -S [ --select ] arg Analyze only these fields. -i [ --individual ] Show results for individual files separately also. --truth arg True value --min arg Required minimum number of lines to read. --mean Show mean and standard deviation. --mode Show mode (with precision) --log-mean Show log mean of X given log X. --median Show median and confidence level. --confidence arg (=0.95) Confidence interval levels (colon-separated). --BCI arg (=HPD) Type of Bayesian Credible Interval (BCI): HPD or central -p [ --precision ] arg (=4) Number of significant figures. Default: Report the median and 95% credible interval for each column. ------- 9/36 stats-select --help OK 0.09s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/stats-select --help --- stdout --- Select columns from a Tracer-format data file. Usage: stats-select [OPTIONS] column-name [column-name ...] < data-file All options: -h [ --help ] Produce help message --no-header Suppress the line of column names. -s [ --select ] arg Select on key=value pairs -r [ --remove ] Remove selected columns, instead of keeping them. -a [ --add ] arg Remove selected columns, instead of keeping them. ------- 10/36 alignment-gild --help OK 0.09s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-gild --help --- stdout --- Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column. Usage: alignment-gild alignment-file tree-file ... [OPTIONS] < alignments-file Allowed options: -h [ --help ] produce help message --align arg file with sequences and initial alignment --tree arg file with initial tree --find-root estimate the root position from branch lengths --alphabet arg set to 'Codons' to prefer codon alphabets --skip arg (=0) number of alignment samples to skip --max-alignments arg (=1000) maximum number of alignments to analyze -V [ --verbose ] Output more log messages on stderr. ------- 11/36 alignment-consensus --help OK 0.09s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-consensus --help --- stdout --- Construct a consensus alignment to summarize an alignment sample. Usage: alignment-consensus [OPTIONS] < alignments-file Allowed options: -h [ --help ] produce help message --alphabet arg Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop. --skip arg (=0) number of tree samples to skip --max-alignments arg (=1000) maximum number of alignments to analyze --strict arg ignore events below this probability --cutoff arg ignore events below this probability --uncertainty arg file-name for AU uncertainty vs level --verbose Output more log messages on stderr. ------- 12/36 alignment-max --help OK 0.09s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-max --help --- stdout --- Construct a posterior decoding alignment to summarize an alignment sample. Usage: alignment-max [OPTIONS] < alignments-file Allowed options: -h [ --help ] Produce help message --alphabet arg Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop. -s [ --skip ] arg (=0) Number of alignment samples to skip -m [ --max-alignments ] arg (=1000) Maximum number of alignments to analyze --analysis arg (=wsum) sum, wsum, wsum2, multiply -o [ --out ] arg (=-) Output file (defaults to stdout) -p [ --out-probabilities ] arg Output file for column probabilities, if specified -V [ --verbose ] Output more log messages on stderr. ------- 13/36 alignment-chop-internal --help OK 0.11s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-chop-internal --help --- stdout --- Remove ancestral sequences from an alignment. Usage: alignment-chop-internal [OPTIONS] < Allowed options: -h [ --help ] produce help message --align arg file with sequences and initial alignment --alphabet arg set to 'Codons' to prefer codon alphabets --tree arg file with tree that specifies leaves to keep -N [ --nleaves ] arg number of sequences to keep ------- 14/36 alignment-indices --help OK 0.08s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-indices --help --- stdout --- Show the alignment in terms of the index of each character in its sequence. Usage: alignment-indices [OPTIONS] Allowed options: -h [ --help ] produce help message --align arg file with sequences and initial alignment --alphabet arg set to 'Codons' to prefer codon alphabets -c [ --columns ] arg Ranges of columns to keep, like: 1-10,30- --invariant arg print only sites where this site and neighbors are invariant. --differences arg how many sequences may differ from the majority? --avoid-gaps arg (=3) How far from a gap must a column be to be invariant? --min-constraints arg Minimum # of constraints per column for a constraint to be emitted ------- 15/36 alignment-info --help OK 0.11s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-info --help --- stdout --- Show useful statistics about the alignment. Usage: alignment-info [] [OPTIONS] Allowed options: -h [ --help ] produce help message --align arg file with sequences and initial alignment --tree arg file with initial tree --alphabet arg specify the alphabet: DNA, RNA, Amino-Acids, Triplets, or Codons -N [ --show-names ] Print the sequence-names and exit -L [ --show-lengths ] Print the sequence-lengths and exit ------- 16/36 alignment-cat --help OK 0.10s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-cat --help --- stdout --- Concatenate several alignments (with the same sequence names) end-to-end. Usage: alignment-cat [ ...] All options: -h [ --help ] Produce help message --output arg (=fasta) Which output format: fasta or phylip? -c [ --columns ] arg Ranges of columns to keep, like: 1-10,30- -t [ --taxa ] arg Taxa to keep, comma-separated -p [ --pad ] Add gaps to make sequence lengths identical -r [ --reverse ] Reverse the sequences -e [ --erase-empty-columns ] Remove columns with no characters (all gaps). --missing arg (=-?) What letters are not characters (e.g. gaps)? --strip-gaps Remove all non-character letters from sequences. --reorder-by-tree arg Reorder the sequences given a tree --use-root use the root specified in the tree file to reorder --reorder-by-alignment arg Reorder the sequences following an alignment --align-by-amino arg Arrange nucleotides into codon alignment Examples: To select columns from an alignment: % alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta % alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta % alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta To concatenate two or more alignments: % alignment-cat filename1.fasta filename2.fasta > all.fasta ------- 17/36 alignment-translate --help OK 0.10s --- command --- 23:24:51 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-translate --help --- stdout --- Translate a DNA/RNA alignment into amino acids. Usage: alignment-translate [OPTIONS] < sequence-file [OPTIONS] Allowed options: -h [ --help ] Produce help message -g [ --genetic-code ] arg (=standard) Specify alternate genetic code. -f [ --frame ] arg (=1) Frame 1, 2, 3, -1, -2, or -3 -r [ --reverse ] Just return the reverse -c [ --complement ] Just return the complement -t [ --translate ] arg (=yes) Translate the sequences Examples: Translate DNA or RNA to amino acids in reading frame 1: % alignment-translate < dna.fasta > aa.fasta Give the reverse complement without translation: % alignment-translate -rc --translate=no < dna.fasta > dna2.fasta The following commands are identical: % alignment-translate --frame=-2 < dna.fasta > aa2.fasta % alignment-translate -rc --frame=2 < dna.fasta > aa2.fasta ------- 18/36 alignment-find --help OK 0.09s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-find --help --- stdout --- Find the last (or first) FASTA alignment in a file. (Alignments are ended by blank lines.) Usage: alignment-find [OPTIONS] < in-file Allowed options: -h [ --help ] produce help message --alphabet arg Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop. --first get the first alignment in the file --last get the last alignment in the file (default) ------- 19/36 trees-consensus --help OK 0.09s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/trees-consensus --help --- stdout --- Find consensus trees and supported splits. Usage: trees-consensus [OPTIONS] [ ... ] Input options: -h [ --help ] Produce help message. -V [ --verbose ] Output more log messages on stderr. -s [ --skip ] arg (=10%) Number of trees to skip. -u [ --until ] arg Read until this number of trees. -m [ --max ] arg Thin tree samples down to this number of trees. -x [ --subsample ] arg (=1) Factor by which to subsample. -i [ --ignore ] arg Comma-separated list of taxa to ignore. Reporting options: --map-trees arg (=1) Only report the top trees per file. --min-support arg (=0.25) Minimum threshold PP for splits. --report arg Write supported partitions to file . --map-tree arg Write out the map tree to file . --consensus arg Write out consensus trees. --greedy-consensus arg Write out greedy consensus trees. --extended-consensus-L arg Write out extended consensus trees + lengths. --extended-consensus arg Write out extended consensus trees. --support-levels arg Write #branches versus LOD to file . --extended-support-levels arg Write #sub-branches versus LOD to file . Search options: --sub-partitions Search for partial splits. --depth arg (=1) Depth at which to look for partial splits. --rooting arg (=0.9) Threshold in search for partial splits. --odds-ratio arg (=1.5) Report partial-splits only if removing taxa improves the odds by at least this ratio. Examples: Compute the majority consensus tree, skipping the first 10% of trees: % trees-consensus newick.trees > c50.tree % trees-consensus newick.trees --skip=10% > c50.tree Skip the first 100 trees: % trees-consensus newick.trees --skip=100 > c50.tree Skip the first 20% of trees and take every 10th tree thereafter: % trees-consensus newick.trees --skip=20% -x10 > c50.tree Compute the 50% (majority) and 80% consensus trees: % trees-consensus newick.trees --consensus=0.5:c50.tree,0.8:c80.tree % trees-consensus newick.trees --consensus=0.5,0.8:c80.tree > c50.tree Compute the MAP tree and write a summary of supported partitions: % trees-consensus --map-tree=MAP.tree --report=partitions.txt Compute the MAP tree and write it to the standard output: % trees-consensus --map-tree=- --report=partitions.txt ------- 20/36 tree-mean-lengths --help OK 0.10s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/tree-mean-lengths --help --- stdout --- Compute the mean lengths for branches in the given topology. Usage: tree-mean-lengths [OPTIONS] [ ...] Allowed options: -h [ --help ] produce help message -T [ --tree ] arg tree to re-root --files arg tree samples to examine -s [ --skip ] arg (=0) number of tree samples to skip -u [ --until ] arg Read until this number of trees. --ignore arg Comma-separated taxa to remove --simple Ignore all branches not in the query tree -x [ --subsample ] arg (=1) factor by which to sub-sample --var report standard deviation of branch lengths instead of mean --no-node-lengths ignore branches not in the specified topology --safe Don't die if no trees match the topology --show-node-lengths Output special format -V [ --verbose ] Output more log messages on stderr. ------- 21/36 mctree-mean-lengths --help OK 0.02s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/mctree-mean-lengths --help --- stdout --- Compute the mean lengths for branches in the given topology. Usage: tree-mean-lengths < in-file Allowed options: -h [ --help ] produce help message --tree arg tree to re-root -s [ --skip ] arg (=0) number of tree samples to skip -u [ --until ] arg Read until this number of trees. --prune arg Comma-separated taxa to remove -x [ --subsample ] arg (=1) factor by which to subsample --var report standard deviation of branch lengths instead of mean --no-node-lengths ignore branches not in the specified topology --safe Don't die if no trees match the topology --drop-partial Remove partial branches --seed arg random seed -V [ --verbose ] Output more log messages on stderr. ------- 22/36 trees-to-SRQ --help OK 0.09s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/trees-to-SRQ --help --- stdout --- Generate Scaled Regeneration Quantile (SRQ) plot Usage: tree-to-srq [ ...] Allowed options: -h [ --help ] produce help message --files arg tree samples to examine --predicates arg predicates to examine -s [ --skip ] arg (=10%) Number of trees to skip. -x [ --subsample ] arg (=1) factor by which to sub-sample -u [ --until ] arg Read until this number of trees. --max-points arg maximum number of points to record --mode arg (=SRQ) SRQ, sum, or values --invert consider the inverse of each event instead --no-scale-x don't scale X --no-scale-y don't scale Y ------- 23/36 pickout --help OK 0.10s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/pickout --help --- stdout --- Generate table from key = value lines in file. Usage: pickout [OPTIONS] [ ... ] < All options: -h [ --help ] Produce help message. -n [ --no-header ] Suppress the line of field names. --large The last value goes to the end of the line. --multi-line The last continues until a blank line. ------- 24/36 cut-range --help OK 0.22s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/cut-range --help --- stdout --- Select lines between certain values of a key. (e.g. iterations) Usage: cut-range [OPTIONS] All options: Invisible options: --filenames arg Filenames to read All options: -h [ --help ] produce help message --key arg (=iterations) cut based on values of =value --skip arg the number of samples to skip --until arg last sample to use --size arg maximum number of samples to use --verbose Output more log messages on stderr. ------- 25/36 trees-distances --help OK 0.09s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/trees-distances --help --- stdout --- Compute autocorrelations or other functions of tree distances. Usage: trees-distances trees-file1 [trees-file2 ...] All options: Input options: -h [ --help ] produce help message -s [ --skip ] arg (=0) number of tree samples to skip -u [ --until ] arg Read until this number of trees. -m [ --max ] arg Thin tree samples down to this number of trees. -x [ --subsample ] arg (=1) factor by which to subsample -V [ --verbose ] Output more log messages on stderr. Analysis options: --analysis arg (=matrix) Analysis: matrix, autocorrelation, diameter, compare, convergence, converged. --metric arg (=topology) Tree distance: topology, branch, internal-branch. --remove-duplicates [matrix]: disallow zero distances between points. --max-lag arg [autocorrelation]: max lag to consider. --CI arg (=0.95) Confidence interval size. --converged arg (=0.05) Comma-separated quantiles of distance required for converged? (smaller is more strict). --mean Show mean and standard deviation --median Show median and confidence interval --minmax Show minimum and maximum distances --leaves-only Show minimum and maximum distances --topology-only Show minimum and maximum distances --jitter arg Amount of noise to add to distances ------- 26/36 alignment-thin --help OK 0.10s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-thin --help --- stdout --- Remove sequences or columns from an alignment. Usage: alignment-thin [OPTIONS] General options: -h [ --help ] Print usage information. -V [ --verbose ] Output more log messages on stderr. Sequence filtering options: -p [ --protect ] arg Sequences that cannot be removed (comma-separated). -k [ --keep ] arg Remove sequences not in comma-separated list . -r [ --remove ] arg Remove sequences in comma-separated list . -l [ --longer-than ] arg Remove sequences not longer than . -s [ --shorter-than ] arg Remove sequences not shorter than . -c [ --cutoff ] arg Remove similar sequences with #mismatches < cutoff. -d [ --down-to ] arg Remove similar sequences down to sequences. --remove-crazy arg Remove outlier sequences -- defined as sequences that are missing too many conserved sites. --conserved arg (=0.75) Fraction of sequences that must contain a letter for it to be considered conserved. Column filtering options: -K [ --keep-columns ] arg Keep columns from this sequence -m [ --min-letters ] arg Remove columns with fewer than letters. -u [ --remove-unique ] arg Remove insertions in a single sequence if longer than letters -e [ --erase-empty-columns ] Remove columns with no characters (all gaps). Output options: -S [ --sort ] Sort partially ordered columns to group similar gaps. -L [ --show-lengths ] Just print out sequence lengths. -N [ --show-names ] Just print out sequence lengths. -F [ --find-dups ] arg For each sequence, find the closest other sequence. Examples: Remove columns without a minimum number of letters: % alignment-thin --min-letters=5 file.fasta > file-thinned.fasta Remove sequences by name: % alignment-thin --remove=seq1,seq2 file.fasta > file2.fasta % alignment-thin --keep=seq1,seq2 file.fasta > file2.fasta Remove short sequences: % alignment-thin --longer-than=250 file.fasta > file-long.fasta Remove similar sequences with <= 5 differences from the closest other sequence: % alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta Remove similar sequences until we have the right number of sequences: % alignment-thin --down-to=30 file.fasta > file-30taxa.fasta Remove dissimilar sequences that are missing conserved columns: % alignment-thin --remove-crazy=10 file.fasta > file2.fasta Protect some sequences from being removed: % alignment-thin --down-to=30 file.fasta --protect=seq1,seq2 > file2.fasta % alignment-thin --down-to=30 file.fasta --protect=@filename > file2.fasta ------- 27/36 alignments-diff --help OK 0.10s --- command --- 23:24:52 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignments-diff --help --- stdout --- Align two alignments for comparison. Usage: alignments-diff alignment-file1 alignment-file2 [OPTIONS] General options: -h [ --help ] produce help message Input options: --alphabet arg set to 'Codons' to prefer codon alphabets Output options: --merge Stack the two alignments into one alignment with duplicate names --dual Write out the two aligned alignments separately --fill arg (=gap) blank columns filled with: gap or unknown -d [ --differences-file ] arg Filename to store differences in AU format --blocksize arg (=20) Width of blocks of same color --classes arg (=1) Number of groups for non-matching characters ------- 28/36 tree-tool --help OK 0.10s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/tree-tool --help --- stdout --- Perform various operations on Newick trees. Usage: tree-tool [OPTIONS] General options: -h [ --help ] produce help message -V [ --verbose ] Output more log messages on stderr. Modification options: --prune arg Comma-separated taxa to remove --root Find a root position --resolve Comma-separated taxa to remove --remove-root-branch Remove single branch from root. --remove-root-branches Ensure root is not a tip. --remove-knuckles Remove degree-2 nodes. --scale arg Scale branch-lengths by factor --strip-internal-names Remove internal node names --name-all-nodes Add node names Output options: --length Report the total tree length --diameter Report the total tree length ------- 29/36 alignment-distances --help OK 0.01s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-distances --help --- stdout --- Compute distances between alignments. Usage: alignment-distances alignments-file1 [alignments-file2 ...] All options: Input options: -h [ --help ] Produce help message -s [ --skip ] arg (=0) Number of alignment samples to skip. -m [ --max ] arg (=1000) Maximum number of alignments to analyze. -V [ --verbose ] Output more log messages on stderr. --alphabet arg Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop. Analysis options: --distances arg (=splits:splits2:nonrecall:inaccuracy) Colon-separated list of distances. --analysis arg Analysis: score, AxA, NxN, compare, median, distances --CI arg (=0.94999999999999996) Confidence interval size. --mean Show mean and standard deviation --median Show median and confidence interval --minmax Show minimum and maximum distances Distances: splits, splits2, pairwise, recall, accuracy, nonrecall, inaccuracy Examples: Compute distances from true.fasta to each in As.fasta: % alignment-distances score true.fasta As.fasta Compute distance matrix between all pairs of alignments in all files: % alignment-distances AxA file1.fasta ... fileN.fasta Compute all NxN pairwise alignment accuracies, averaged over As: % alignment-distances NxN true.fasta As.fasta Find alignment with smallest average distance to other alignments: % alignment-distances median As.fasta A.fasta Compare the distances with-in and between the two groups: % alignment-distances compare A-dist1.fasta A-dist2.fasta Report distribution of average distance to other alignments: % alignment-distances distances As.fasta A.fasta ------- 30/36 alignment-draw --help OK 0.02s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/alignment-draw --help --- stdout --- Draw an alignment to HTML, optionally coloring residues by AU. Usage: alignment-draw [] [OPTIONS] All options: General options: -h [ --help ] produce help message --file arg file with sequences and initial alignment Output: --legend Print a legend showing how color-scheme indicates uncertainty. --show-ruler Print a ruler to show column numbers --column-colors Color-code column ticks by column certainty --AU arg file with alignment uncertainties --show-gaps arg (=yes) Show gaps --gaps-different arg (=yes) Color gaps in grey. --width arg The number of columns per line --start arg The first column to plot --end arg The last column to plot --format arg (=HTML) produce a plot in this format --min arg Minimum value of scale function --max arg Maximum value of scale function --color-scheme arg Include a length of how certainties map to colors --scale arg (=LOD) scale for the uncertainties Base Color Schemes: plain, bw, Rainbow, RedBlue, BlueRed, AA, DNA Modifiers: switch, contrast, fade Examples: Rainbow+contrast+fade AA+contrast+fade+fade+fade+fade ------- 31/36 trees-bootstrap --help OK 0.10s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/trees-bootstrap --help --- stdout --- Compare support for partitions between different files. Usage: trees-bootstrap [ ... ] --predicates [OPTIONS] All options: Input options: -h [ --help ] Produce help message. -s [ --skip ] arg (=10%) Number of trees to skip. -u [ --until ] arg Read until this number of trees. -m [ --max ] arg Thin tree samples down to this number of trees. -x [ --subsample ] arg Factor by which to sub-sample. --predicates arg Predicates to examine. --min-support arg (=0.1) Minimum value of predicates to consider interesting.. -V [ --verbose ] Output more log messages on stderr. Block bootstrap options: --bootstrap Do block bootstrapping to get a CI on the posterior probabilities. --samples arg (=10000) Number of bootstrap samples. --pseudocount arg (=1) Extra 0/1 to add to bootstrap samples. --blocksize arg Block size to use in block boostrap. --seed arg Random seed. Reporting options: --separation arg (=0) Only report trees/partitions if they differ by this many LODs --confidence arg (=0.95) Width of confidence intervals --LOD-table arg Write the partitions LOD10's to a file. ------- 32/36 draw-tree --help OK 0.21s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/draw-tree --help --- stdout --- Draw NEWICK (and some other) formatted files. Usage: draw-tree [OPTIONS] All options: Input options: -h [ --help ] Produce help message -W [ --width ] arg (=8.5) Page width in inches -H [ --height ] arg (=11) Page height in inches --file arg predicates to examine --output arg (=pdf) Type of output to write: tree, topology, mtree, lengths, dot, ps, pdf, svg --out arg Output filename (without extension) --full Consider only full splits by collapsing any partial splits. --iterations arg (=2) Number of iterations for layout algorithm --font-size arg (=10) Font size for taxon names --angle_iterations arg (=0) Number of iterations for layout algorithm with small-angle penalties --labels arg (=horizontal) Are the names horizontal or angled? --collapse Give node lengths evenly to neighboring branches and zero the node lengths. --layout arg (=graph) Layout method: graph, equal-angle, equal-daylight, etc. --greedy For equal-daylight layout: take as much daylight as possible? --tree-layout-initial Start an energy layout with positions from the equal-angle layout - only for multifurcating trees --no-shade For equal-daylight layout: reject rotations that shade other groups? --draw-clouds arg Draw wandering-ranges in MC trees as clouds. --seed arg Random seed --verbose Output more log messages on stderr. ------- 33/36 extract-ancestors --help OK 0.07s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/extract-ancestors --help --- stdout --- Extract and name ancestral sequences according to node- and branch- queries. Usage: extract-ancestors [OPTIONS] All options: General options: -h [ --help ] produces help message -V [ --verbose ] [=arg(=1)] Show more log messages on stderr. Input options: -A [ --alignments ] arg File of alignment samples -T [ --trees ] arg File of corresponding tree samples -x [ --subsample ] arg (=10) factor by which to sub-sample trees Ancestor query options: -n [ --nodes ] arg Newick tree with labelled ancestors -g [ --groups ] arg File with named groups --nodes-min arg (=0.34) Minimum fraction to include a node. --groups-min arg (=0.34) Minimum fraction to include a group. Examples: Add named ancestral sequences to alignments where they are present: % extract-ancestors -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree ------- 34/36 summarize-ancestors --help OK 0.09s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/summarize-ancestors --help --- stdout --- Construct alignments with internal sequences for labeled nodes in query tree. Usage: summarize-ancestors -A -T [OPTIONS] All options: General options: -h [ --help ] produces help message -V [ --verbose ] [=arg(=1)] Show more log messages on stderr. Input options: -A [ --alignments ] arg File of alignment samples -T [ --trees ] arg File of corresponding tree samples -x [ --subsample ] arg (=10) factor by which to sub-sample trees -m [ --max ] arg (=500) Thin (alignment,tree) pairs down to this number of samples. Ancestor query options: -n [ --nodes ] arg Newick tree with labelled ancestors -g [ --groups ] arg File with named groups --nodes-min arg (=0.34) Minimum fraction to include a node. --groups-min arg (=0.34) Minimum fraction to include a group. Examples: Add ancestral sequences to summary alignment: % summarize-ancestors summary.fasta -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree ------- 35/36 subsample --help OK 0.01s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-subsample --help --- stdout --- Subsample lines in a file. Usage: subsample [OPTIONS] < in-file Allowed options: -h [ --help ] produce help message -x [ --factor ] arg (=1) Factor by which to subsample. --skip arg (=0) Throw out some lines at the beginning. --max arg Maximum number of samples to keep --header This file has a header - don't throw it out. ------- 36/36 bali-phy testsuite OK 517.90s --- command --- 23:24:53 /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/tests/run-tests.py /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/bali-phy/bali-phy --package-path=/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg/obj-x86_64-linux-gnu/src/builtins:/build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg --- stdout --- Running tests for 'bali-phy': Running test: mcmc/one-sequence/1 ... ok Running test: mcmc/with-imodel ... ok Running test: mcmc/no-imodel ... ok Running test: mcmc/fixed-scale ... ok Running test: mcmc/two-sequences/1 ... ok Running test: haskell/IO/3 ... ok Running test: haskell/IO/1 ... ok Running test: haskell/parse/1 ... ok Running test: haskell/Ord/3 ... ok Running test: haskell/Ord/2 ... ok Running test: haskell/Ord/1 ... ok Running test: haskell/Data/Map ... ok Running test: IO/errors/Triplets/AUTGC ... ok Running test: IO/errors/Triplets/2 ... ok Running test: IO/errors/Triplets/1 ... ok Running test: IO/errors/DNA-RNA/3 ... ok Running test: IO/errors/DNA-RNA/2 ... ok Running test: IO/errors/DNA-RNA/1 ... ok Running test: IO/errors/Codons/3 ... ok Running test: IO/errors/Codons/AUTGC ... ok Running test: IO/errors/Codons/2 ... ok Running test: IO/errors/Codons/stop/2 ... ok Running test: IO/errors/Codons/stop/1 ... ok Running test: IO/errors/Codons/1 ... ok Running test: prob_prog/categorical ... ok Running test: prob_prog/functions/1 ... ok Running test: prob_prog/infer_tree/1 ... ok Running test: prob_prog/popgen/li_stephens ... ok Running test: prob_prog/observe/1 ... ok Running test: prob_prog/lazy_sample/3 ... ok Running test: prob_prog/lazy_sample/2 ... ok Running test: prob_prog/lazy_sample/1 ... ok Running test: prob_prog/if-then-else/1 ... ok Running test: prob_prog/order-two ... ok Running test: prob_prog/regression ... ok Running test: prob_prog/sample_crp ... ok Running test: prob_prog/demos/airline ... ok Running test: prob_prog/demos/5 ... ok Running test: prob_prog/demos/3 ... ok Running test: prob_prog/demos/coalmine ... ok Running test: prob_prog/demos/2 ... ok Running test: prob_prog/demos/6 ... ok Running test: prob_prog/demos/1 ... ok Running test: prob_prog/demos/4 ... ok Running test: prob_prog/sample_tree/3 ... ok Running test: prob_prog/sample_tree/2 ... ok Running test: prob_prog/sample_tree/1 ... ok Running test: parse/constraints/1 ... FAIL! ['exit'] (expected) evaluating reg # 8552: case <8553> of {SModel.ReversibleMarkov.ReversibleMarkov h i j k l m n -> h; SModel.F81 h i j k -> h; SModel.MixtureModel h -> SModel.getAlphabet (SModel.baseModel (SModel.MixtureModel h) SModel.#365); SModel.MixtureModels h i -> case i of {j:k -> SModel.getAlphabet j; _ -> SModel.#348}; _ -> SModel.#348} evaluating reg # 8662: Prelude:add <8689> <12993> Add: object 'SModel.ReversibleMarkov.ReversibleMarkov %5 %3 %2 %4 %1 %6 %0' is not double, int, log_double, or char' Running test: parse/functions/1 ... ok Running test: parse/M3/2 ... ok Running test: parse/M3/1 ... ok Running test: parse/18 ... ok Running test: parse/9 ... ok Running test: parse/error/3 ... ok Running test: parse/error/2 ... ok Running test: parse/error/1 ... ok Running test: parse/error/4 ... ok Running test: parse/int-to-double/3 ... ok Running test: parse/int-to-double/2 ... ok Running test: parse/int-to-double/1 ... ok Running test: parse/24 ... ok Running test: parse/5 ... ok Running test: parse/partitions/link/9 ... ok Running test: parse/partitions/link/5 ... ok Running test: parse/partitions/link/3 ... ok Running test: parse/partitions/link/8 ... ok Running test: parse/partitions/link/2 ... ok Running test: parse/partitions/link/6 ... ok Running test: parse/partitions/link/7 ... ok Running test: parse/partitions/link/1 ... ok Running test: parse/partitions/link/4 ... ok Running test: parse/partitions/3 ... ok Running test: parse/partitions/2 ... ok Running test: parse/partitions/1 ... ok Running test: parse/partitions/4 ... ok Running test: parse/3 ... ok Running test: parse/13 ... ok Running test: parse/19 ... ok Running test: parse/17 ... ok Running test: parse/8 ... ok Running test: parse/14 ... ok Running test: parse/21 ... ok Running test: parse/x3/5 ... ok Running test: parse/x3/3 ... ok Running test: parse/x3/2 ... ok Running test: parse/x3/1 ... ok Running test: parse/x3/4 ... ok Running test: parse/22 ... ok Running test: parse/12 ... ok Running test: parse/11 ... ok Running test: parse/26 ... ok Running test: parse/let/1 ... ok Running test: parse/16 ... ok Running test: parse/25 ... ok Running test: parse/6 ... ok Running test: parse/7 ... ok Running test: parse/10 ... ok Running test: parse/4 ... ok Running test: parse/23 ... ok Running test: parse/guess-alphabet/aa ... ok Running test: parse/guess-alphabet/rna ... ok Running test: parse/guess-alphabet/Triplets/rna ... ok Running test: parse/guess-alphabet/Triplets/dna ... ok Running test: parse/guess-alphabet/dna ... ok Running test: parse/guess-alphabet/Codons/rna ... ok Running test: parse/guess-alphabet/Codons/dna ... ok Running test: optimizer/15 ... ok Running test: optimizer/9 ... ok Running test: optimizer/eta-reduction ... ok Running test: optimizer/5 ... ok Running test: optimizer/3 ... ok Running test: optimizer/13 ... ok Running test: optimizer/8 ... ok Running test: optimizer/14 ... ok Running test: optimizer/2 ... ok Running test: optimizer/12 ... FAIL! ['error'] (expected) Running test: optimizer/11 ... FAIL! ['error'] (expected) Running test: optimizer/16 ... FAIL! ['error'] (expected) Running test: optimizer/pat-bind ... ok Running test: optimizer/6 ... ok Running test: optimizer/7 ... ok Running test: optimizer/1 ... ok Running test: optimizer/10 ... ok Running test: optimizer/4 ... ok Running test: print/2 ... ok Running test: print/1 ... ok SUCCESS! (0 unexpected failures, 4 expected failures, 126 tests total) ------- Summary of Failures: 3/36 bali-phy 5d test TIMEOUT 30.25s Ok: 35 Expected Fail: 0 Fail: 0 Unexpected Pass: 0 Skipped: 0 Timeout: 1 dh_auto_test: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 meson test returned exit code 1 make: *** [debian/rules:20: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 E: run_chroot failed: E: command failed: chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bali-phy-kUKYaG/bali-phy-3.6.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1612666578" dpkg-buildpackage -uc -a amd64 --build=any" W: listening on child socket failed: I: removing tempdir /tmp/mmdebstrap.w0hk_H1ON8... mmdebstrap failed