Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/prime-phylo/prime-phylo_1.0.11-9+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/prime-phylo-1.0.11-9+b169hj_bzd/prime-phylo_1.0.11-9+b1_amd64.buildinfo Get source package info: prime-phylo=1.0.11-9 Source URL: http://snapshot.notset.fr/mr/package/prime-phylo/1.0.11-9/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-11.1 automake=1:1.16.3-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1-1 binutils=2.35.1-4 binutils-common=2.35.1-4 binutils-x86-64-linux-gnu=2.35.1-4 bison=2:3.7.4+dfsg-1 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-2 build-essential=12.8 bzip2=1.0.8-4 cmake=3.18.4-1+b1 cmake-data=3.18.4-1 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-1 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.3 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 flex=2.6.4-8 g++=4:10.2.0-1 g++-10=10.2.1-1 gcc=4:10.2.0-1 gcc-10=10.2.1-1 gcc-10-base=10.2.1-1 gengetopt=2.23+dfsg1-1 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gfortran=4:10.2.0-1 gfortran-10=10.2.1-1 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 ibverbs-providers=32.0-1+b1 icu-devtools=67.1-5 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.1-1 libatomic1=10.2.1-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1+b1 libbinutils=2.35.1-4 libblas-dev=3.9.0-3 libblas3=3.9.0-3 libblkid1=2.36.1-2 libboost-dev=1.74.0.2 libboost-mpi-dev=1.74.0.2 libboost-mpi1.74-dev=1.74.0-3+b1 libboost-mpi1.74.0=1.74.0-3+b1 libboost-serialization-dev=1.74.0.2 libboost-serialization1.74-dev=1.74.0-3+b1 libboost-serialization1.74.0=1.74.0-3+b1 libboost1.74-dev=1.74.0-3+b1 libbrotli1=1.0.9-2+b2 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-5 libc-dev-bin=2.31-5 libc6=2.31-5 libc6-dev=2.31-5 libcap-ng0=0.7.9-2.2+b1 libcbor0=0.5.0+dfsg-2 libcc1-0=10.2.1-1 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-4 libctf0=2.35.1-4 libcurl4=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdpkg-perl=1.20.5 libedit2=3.1-20191231-1 libelf1=0.182-1 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.2.10-1 libfabric1=1.11.0-2 libffi7=3.3-5 libfido2-1=1.5.0-2 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.1-1 libgcc-s1=10.2.1-1 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran-10-dev=10.2.1-1 libgfortran5=10.2.1-1 libglib2.0-0=2.66.3-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-3 libgomp1=10.2.1-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libhwloc-dev=2.4.0+dfsg-2 libhwloc-plugins=2.4.0+dfsg-2 libhwloc15=2.4.0+dfsg-2 libibverbs-dev=32.0-1+b1 libibverbs1=32.0-1+b1 libicu-dev=67.1-5 libicu67=67.1-5 libidn2-0=2.3.0-4 libisl23=0.23-1 libitm1=10.2.1-1 libjs-jquery=3.5.1+dfsg+~3.5.4-3 libjs-jquery-ui=1.12.1+dfsg-7 libjsoncpp24=1.9.4-3 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.1-1 libltdl-dev=2.4.6-14 libltdl7=2.4.6-14 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-1 libncursesw6=6.2+20201114-1 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.12-1+b1 libnuma1=2.0.12-1+b1 libopenmpi-dev=4.0.5-7 libopenmpi3=4.0.5-7 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpciaccess0=0.16-1 libpcre2-8-0=10.35-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpmix-dev=3.2.2~rc1-1 libpmix2=3.2.2~rc1-1 libprocps8=2:3.3.16-5 libpsl5=0.21.0-1.1 libpsm-infinipath1=3.3+20.604758e7-6+b1 libpsm2-2=11.2.185-1 libquadmath0=10.2.1-1 librdmacm1=32.0-1+b1 librhash0=1.4.0-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3+b1 libselinux1=3.1-2+b2 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsepol1=3.1-1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-2 libssh2-1=1.9.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-1 libstdc++6=10.2.1-1 libsub-override-perl=0.09-2 libsystemd0=247.1-3 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.1-1 libubsan1=10.2.1-1 libuchardet0=0.0.7-1 libucx0=1.9.0~rc1-2 libudev1=247.1-3 libunistring2=0.9.10-4 libuuid1=2.36.1-2 libuv1=1.40.0-1 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxml2=2.9.10+dfsg-6.3+b1 libxml2-dev=2.9.10+dfsg-6.3+b1 libxnvctrl0=450.80.02-1+b1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.11-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 mpi-default-dev=1.13 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 node-jquery=3.5.1+dfsg+~3.5.4-3 ocl-icd-libopencl1=2.2.13-1 openmpi-bin=4.0.5-7 openmpi-common=4.0.5-7 openssh-client=1:8.4p1-3 passwd=1:4.8.1-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 procps=2:3.3.16-5 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 util-linux=2.36.1-2 xz-utils=5.2.4-1+b1 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/20201212T153433Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201210T083846Z/ 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 prime-phylo=1.0.11-9 && mkdir -p /build/prime-phylo-ElMCOa && dpkg-source --no-check -x /*.dsc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 && cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 && { printf '%s' 'prime-phylo (1.0.11-9+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against boost 1.74 -- all / amd64 / i386 Build Daemon (x86-conova-01) Sat, 12 Dec 2020 17:12:53 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/prime-phylo-ElMCOa" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607793173" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/prime-phylo-ElMCOa /tmp/prime-phylo-1.0.11-9+b169hj_bzd bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201210T083846Z 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.hMBHdmlvuO 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.hMBHdmlvuO Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-2). 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/20201210T083846Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201210T083846Z 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 (833 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 ... 4616 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 (2.31-5) ... 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/20201212T153433Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201210T083846Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.hMBHdmlvuO Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201210T083846Z 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/20201212T153433Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201212T153433Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 30s (1146 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.hMBHdmlvuO I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d prime-phylo=1.0.11-9 && mkdir -p /build/prime-phylo-ElMCOa && dpkg-source --no-check -x /*.dsc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 && cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 && { printf '%s' 'prime-phylo (1.0.11-9+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against boost 1.74 -- all / amd64 / i386 Build Daemon (x86-conova-01) Sat, 12 Dec 2020 17:12:53 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/prime-phylo-ElMCOa"' exec /tmp/mmdebstrap.hMBHdmlvuO Reading package lists... NOTICE: 'prime-phylo' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/prime-phylo.git Please use: git clone https://salsa.debian.org/med-team/prime-phylo.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 759 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main prime-phylo 1.0.11-9 (dsc) [2177 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main prime-phylo 1.0.11-9 (tar) [751 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main prime-phylo 1.0.11-9 (diff) [6436 B] Fetched 759 kB in 1s (1144 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'prime-phylo_1.0.11-9.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting prime-phylo in /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-Boost160.patch dpkg-source: info: applying fix-gcc-8.patch dpkg-source: info: applying 0003-Fix-build-with-Boost-1.67.patch dpkg-source: info: applying 0004-fix-gcc10-build.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607793173" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.hMBHdmlvuO dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-9+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary-arch dh binary-arch --buildsystem=cmake dh_update_autotools_config -a -O--buildsystem=cmake dh_autoreconf -a -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11' dh_auto_configure -- \ -Dofficial_binary_packaging=on \ -Dprime_dynamic=on \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \ -DCMAKE_BUILD_TYPE=RELEASE cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. -- The CXX compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- The Fortran compiler identification is GNU 10.2.1 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 - yes -- The C compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so hittade /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for Fortran cheev -- Looking for Fortran cheev - not found -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. -- Found BISON: /usr/bin/bison (found version "3.7.4") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.40.0") found components: mpi serialization -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.10") mpilib is /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include included path is CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDTLSR". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDTLSR/CMakeLists.txt:30 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDLRS". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDLRS/CMakeLists.txt:27 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "showtree". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/tools/showtree/CMakeLists.txt:12 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:120 (if): Policy CMP0053 is not set: Simplify variable reference and escape sequence evaluation. Run "cmake --help-policy CMP0053" for policy details. Use the cmake_policy command to set the policy and suppress this warning. For input: '@CMAKE_SOURCE_DIR@/excluded_from_release' the old evaluation rules produce: '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/excluded_from_release' but the new evaluation rules produce: '@CMAKE_SOURCE_DIR@/excluded_from_release' Using the old result for compatibility since the policy is not set. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11' dh_auto_build -a -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-ElMCOa/prime-phylo-1.0.11 -B/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 0%] [BISON][MyParser2] Building parser with bison 3.7.4 [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/flex -o/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l gb.y: warning: 1 nonterminal useless in grammar [-Wother] gb.y: warning: 1 rule useless in grammar [-Wother] gb.y:258.1-12: warning: nonterminal useless in grammar: darwin_entry [-Wother] 258 | darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */} | ^~~~~~~~~~~~ cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake --color= Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend.internal". Scanning dependencies of target prime-phylo-sfile make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o [ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c: In function ‘main’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] 17 | if (!strcmp(argv[opt], "-d")) { | ^~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:265:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] 265 | printf("%9d", char_counter + 1); | ^~~~~ ~~~~~~~~~~~~~~~~ | | | long int /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable ‘date’ set but not used [-Wunused-but-set-variable] 212 | char *top, *date; | ^~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c: In function ‘yyparse’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1093:16: warning: implicit declaration of function ‘yylex’ [-Wimplicit-function-declaration] 1093 | yychar = yylex (); | ^~~~~ gb.y: In function ‘yyerror’: gb.y:291:70: warning: implicit declaration of function ‘linenumber’ [-Wimplicit-function-declaration] gb.y: In function ‘add_to_seq’: gb.y:402:9: warning: unused variable ‘new_buf’ [-Wunused-variable] seqreader.l: In function ‘seq_read’: seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable] At top level: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function] 1864 | static int input (void) | ^~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: ‘yyunput’ defined but not used [-Wunused-function] 1821 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ [ 4%] Linking C shared library libprime-phylo-sfile.so cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so CMakeFiles/prime-phylo-sfile.dir/gbread.c.o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -Wl,-rpath,:::::::::::::::::::: make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 4%] [BISON][MyParser] Building parser with bison 3.7.4 cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y NHXparse.y:105.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] 105 | %expect 4 | ^~~~~~~ [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake --color= Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend.internal". Scanning dependencies of target prime-phylo make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function ‘NHX_debug_print’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c:155:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] 155 | fprintf(stderr, "BW:\t%d\n", l->arg.t); | ~^ ~~~~~~~~ | | | | int double | %f /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16: warning: ‘input’ defined but not used [-Wunused-function] 1597 | static int input (void) | ^~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17: warning: ‘yyunput’ defined but not used [-Wunused-function] 1554 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ In file included from /usr/include/string.h:495, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c:4: In function ‘strncpy’, inlined from ‘new_annotation’ at /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c:80:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 5 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c: In function ‘yytree_parse’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:69:25: warning: implicit declaration of function ‘yytree_lex’ [-Wimplicit-function-declaration] 69 | #define yylex yytree_lex | ^~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:1109:16: note: in expansion of macro ‘yylex’ 1109 | yychar = yylex (); | ^~~~~ NHXparse.y: In function ‘read_tree’: NHXparse.y:351:5: warning: implicit declaration of function ‘close’; did you mean ‘pclose’? [-Wimplicit-function-declaration] NHXparse.y: In function ‘read_tree_string’: NHXparse.y:399:3: warning: implicit declaration of function ‘read_from_string’; did you mean ‘read_tree_string’? [-Wimplicit-function-declaration] NHXparse.y:404:3: warning: implicit declaration of function ‘close_string_buffer’ [-Wimplicit-function-declaration] [ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Hacks.cc [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc:4: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function ‘void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:23: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 405 | catch(std::exception e) | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:23: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 423 | catch(std::exception e) | ^ [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TimeEstimator.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.cc [ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o 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-O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscTree.cc [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/InvMRCA.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ [ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Node.cc [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.cc [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/RandomTreeGenerator.cc [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/StrStrMap.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc [ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizer.cc [ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizers.cc [ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc [ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc: In constructor ‘beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const Real&)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:26:15: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null] 26 | old_times(NULL), | ^~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:6, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:27:15: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null] 27 | old_rates(NULL), | ^~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:6, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:28:17: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null] 28 | old_lengths(NULL), | ^~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:6, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function ‘void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:118:22: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null] 118 | buf[ bytes_read ]=NULL; | ^~~~ [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function ‘beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector*, beep::StrStrMap*, std::map*, std::map*)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:22: warning: ‘idInt’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1049 | new_node = S.addNode(l, r, idInt, name); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:6: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.cc [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC.cc [ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function ‘void beep::EdgeRateMCMC_common::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable ‘fparam’ [-Wunused-variable] 104 | Real fparam = std::log(rate) - 0.5 * variance * (rtime - 3.0 * ltime); | ^~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable ‘rparam’ [-Wunused-variable] 105 | Real rparam = variance * (rtime + ltime); | ^~~~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function ‘void beep::EdgeWeightMCMC::showCurrentTree()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 106 | for (int i = 0; i < t.size(); i++) | ~~^~~~~~~~~~ [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc [ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCModel.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCObject.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:6: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc: In member function ‘virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable ‘check_number_nonupdate’ set but not used [-Wunused-but-set-variable] 78 | unsigned check_number_nonupdate = 0; | ^~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.cc [ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/MCMCSampler.cc [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/GSRSampler.cc [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleObserver.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc [ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function ‘virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on ‘i’ may be undefined [-Wsequence-point] 338 | p[++i] = geneFams[i]->initStateProb();//updateDataProbability(); | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on ‘i’ may be undefined [-Wsequence-point] /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on ‘i’ may be undefined [-Wsequence-point] [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc [ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor ‘beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: ‘beep::EdgeDiscGSR::m_calculatedAtAndBelow’ will be initialized after [-Wreorder] 588 | bool m_calculatedAtAndBelow; | ^~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: ‘bool beep::EdgeDiscGSR::m_calculatedAtBars’ [-Wreorder] 583 | bool m_calculatedAtBars; | ^~~~~~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, | ^~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function ‘void beep::EdgeDiscGSR::convertDensitiesToProbabilities()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 475 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable ‘xpt’ set but not used [-Wunused-but-set-variable] 485 | Point xpt = x.getPt(); | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 525 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable ‘parent’ [-Wunused-variable] 528 | Node *parent = u->getParent(); | ^~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function ‘beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable ‘timeStep’ [-Wunused-variable] 897 | Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first); | ^~~~~~~~ [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::ABS_TOL’ of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::ABS_TOL’ of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::ABS_TOL’ of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc [ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.cc [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘unsigned int beep::fastGEM::calcMaxProb(unsigned int)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:136:14: warning: variable ‘topRateProb’ set but not used [-Wunused-but-set-variable] 136 | Probability topRateProb = df->operator()(rate); | ^~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printSa()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1298:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1298 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLb()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1325:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1325 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLt()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1356:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1356 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ [ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc [ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function ‘void beep::ReconciliationSampler::setAttributesAndProbabilities()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 161 | Probability p = calculateDataProbability(); | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function ‘std::string beep::ReconciliationTimeModel::table4os() const’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef ‘MapIter’ locally defined but not used [-Wunused-local-typedefs] 319 | typedef std::map::const_iterator MapIter; | ^~~~~~~ [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function ‘const string beep::ReconciliationTimeSampler::table4os() const’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef ‘MapIter’ locally defined but not used [-Wunused-local-typedefs] 422 | typedef std::map::const_iterator MapIter; | ^~~~~~~ [ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor ‘beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const string&)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: ‘beep::ReconciliationTreeGenerator::R’ is initialized with itself [-Winit-self] 31 | ReconciliationTreeGenerator:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function ‘beep::Tree& beep::HybridTree::getBinaryTree() const’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:367:40: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] 367 | if(rootNode && bTree.getRootNode() == false) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc [ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc In file included from /usr/include/c++/10/ext/hash_map:60, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.cc [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SeqIO.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SeqIO.cc [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: ‘std::ostream& beep::operator<<(std::ostream&, const beep::SequenceType&)’ has not been declared within ‘beep’ 270 | ostream& beep::operator<<(ostream& os, const SequenceType& dt) | ^~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:8: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a ‘friend’ 56 | friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); | ^~~~~~~~ [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc [ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function ‘std::map beep::SequenceData::getBaseFrequencies()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 288 | for (int i = 0; i < seqType.alphabetSize(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:303:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 303 | for (int j = 0; j < seq.length(); j++) { | ~~^~~~~~~~~~~~~~ [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor ‘beep::LA_Matrix::LA_Matrix()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:19:5: warning: ‘beep::LA_Matrix::dim’ is initialized with itself [-Winit-self] 19 | LA_Matrix::LA_Matrix() | ^~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor ‘beep::LA_Matrix::LA_Matrix()’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:20:13: warning: ‘*.beep::LA_Matrix::dim’ is used uninitialized in this function [-Wuninitialized] 20 | : dim(dim), | ^~~ [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc [ 81%] Linking CXX shared library libprime-phylo.so cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo.so -o libprime-phylo.so CMakeFiles/prime-phylo.dir/NHXnode.c.o CMakeFiles/prime-phylo.dir/NHXtree.c.o CMakeFiles/prime-phylo.dir/NHXannotation.c.o CMakeFiles/prime-phylo.dir/lexer.c.o CMakeFiles/prime-phylo.dir/NHXparse.c.o CMakeFiles/prime-phylo.dir/AnError.cc.o CMakeFiles/prime-phylo.dir/Beep.cc.o CMakeFiles/prime-phylo.dir/BeepOption.cc.o CMakeFiles/prime-phylo.dir/Hacks.cc.o CMakeFiles/prime-phylo.dir/ODESolver.cc.o CMakeFiles/prime-phylo.dir/PRNG.cc.o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o CMakeFiles/prime-phylo.dir/Probability.cc.o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o CMakeFiles/prime-phylo.dir/DiscTree.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o CMakeFiles/prime-phylo.dir/EpochTree.cc.o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o CMakeFiles/prime-phylo.dir/Node.cc.o CMakeFiles/prime-phylo.dir/NodeMap.cc.o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o CMakeFiles/prime-phylo.dir/Tree.cc.o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o CMakeFiles/prime-phylo.dir/TreeIO.cc.o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o CMakeFiles/prime-phylo.dir/SimpleML.cc.o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o CMakeFiles/prime-phylo.dir/GammaMap.cc.o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/fastGEM.cc.o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o CMakeFiles/prime-phylo.dir/HybridTree.cc.o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o CMakeFiles/prime-phylo.dir/SeqIO.cc.o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o CMakeFiles/prime-phylo.dir/SequenceType.cc.o CMakeFiles/prime-phylo.dir/SequenceData.cc.o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -L/usr/lib/x86_64-linux-gnu/liblapack.so -L/usr/lib/x86_64-linux-gnu/libblas.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu/liblapack.so:/usr/lib/x86_64-linux-gnu/libblas.so:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../sfile/libprime-phylo-sfile.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 81%] Built target prime-phylo make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color= make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 82%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". [ 83%] Generating cmdline.c, cmdline.h Scanning dependencies of target primeDLRS cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' Scanning dependencies of target primeDTLSR make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 83%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= [ 83%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc Scanning dependencies of target primeGEM Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' Scanning dependencies of target treesize make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 83%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc [ 83%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/treesize.dir/treesize.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc: In function ‘int main(int, char**)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:55:13: warning: enumeration value ‘input_format__NULL’ not handled in switch [-Wswitch] 55 | switch(args_info.input_format_arg) | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:90:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 90 | catch (AnError e) { | ^ [ 84%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.c [ 85%] Linking CXX executable treesize cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 85%] Built target treesize make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 85%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake --color= Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". Scanning dependencies of target showtree make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:14: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function ‘void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:30:20: warning: variable ‘nw’ set but not used [-Wunused-but-set-variable] 30 | bool et, nt, bl, nw; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function ‘int main(int, char**)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 197 | catch(AnError e) | ^ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::EpochBDTProbs::ABS_TOL’ of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function ‘int main(int, char**)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:174:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 174 | if(args_info.tree_number_arg >= Tvec.size()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:198:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 198 | catch (AnError e) | ^ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:16: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:17: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 86%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/showtree.dir/cmdline.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c [ 87%] Linking CXX executable showtree cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so [ 88%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 88%] Built target showtree make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 89%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile 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Scanning dependencies of target reconcile make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 90%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc [ 90%] Linking CXX executable primeGEM cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 90%] Built target primeGEM make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 91%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reroot /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake --color= Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend.internal". 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Scanning dependencies of target reroot make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 91%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reroot.dir/reroot.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc [ 92%] Linking CXX executable primeDLRS cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 [ 92%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 92%] Built target primeDLRS make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 92%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color= Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend.internal". 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Scanning dependencies of target tree2leafnames make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 93%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc [ 94%] Linking CXX executable primeDTLSR cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 94%] Built target primeDTLSR make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 94%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-ElMCOa/prime-phylo-1.0.11 /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color= Dependee "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend.internal". 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Scanning dependencies of target chainsaw make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build make[3]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 95%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function ‘int main(int, char**)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value ‘input_format__NULL’ not handled in switch [-Wswitch] 76 | switch(args_info.input_format_arg) | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:181:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 181 | catch (AnError e) { | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function ‘int main(int, char**)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value ‘input_format__NULL’ not handled in switch [-Wswitch] 51 | switch(args_info.input_format_arg) | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:95:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 95 | catch (AnError e) { | ^ [ 96%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c [ 96%] Linking CXX executable tree2leafnames cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 96%] Built target tree2leafnames [ 96%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function ‘int main(int, char**)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 37 | char *ofilename = "mpr.out"; | ^~~~~~~~~ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 128 | catch (AnError e) { | ^ [ 97%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function ‘void populateGsMap(beep::Tree, beep::StrStrMap&)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 157 | for (int i = 0; i < gtree.getNumberOfNodes(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.c /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value ‘guest_tree_format__NULL’ not handled in switch [-Wswitch] 90 | switch(ai.guest_tree_format_arg) | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘beep::Tree ReadHostTree(gengetopt_args_info&)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:114:9: warning: enumeration value ‘host_tree_format__NULL’ not handled in switch [-Wswitch] 114 | switch(ai.host_tree_format_arg) | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘int main(int, char**)’: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:163:17: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 163 | catch (AnError e) { | ^ /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:188:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 188 | catch (AnError e) { | ^ [ 99%] Linking CXX executable reroot cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so [ 99%] Linking CXX executable reconcile cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 99%] Built target reroot make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 99%] Built target reconcile [100%] Linking CXX executable chainsaw cd /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [100%] Built target chainsaw make[2]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' dh_auto_test -a -O--buildsystem=cmake create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=cmake dh_prep -a -O--buildsystem=cmake dh_auto_install -a -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-ElMCOa/prime-phylo-1.0.11 -B/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Debug" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/chainsaw.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDLRS.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeGEM.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reconcile.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reroot.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/showtree.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/treesize.1 -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw -- Set runtime path of "/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-ElMCOa/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/mcmc_analysis make[1]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11/obj-x86_64-linux-gnu' dh_installdocs -a -O--buildsystem=cmake dh_installchangelogs -a -O--buildsystem=cmake dh_installman -a -O--buildsystem=cmake dh_installsystemduser -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -a -O--buildsystem=cmake dh_strip -a -a -O--buildsystem=cmake debian/rules override_dh_makeshlibs make[1]: Entering directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11' dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so make[1]: Leaving directory '/build/prime-phylo-ElMCOa/prime-phylo-1.0.11' dh_shlibdeps -a -a -O--buildsystem=cmake dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-9+b1_amd64.deb'. dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-9+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../prime-phylo_1.0.11-9+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/prime-phylo-ElMCOa /tmp/prime-phylo-1.0.11-9+b169hj_bzd I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.hMBHdmlvuO... I: success in 1469.0096 seconds md5: prime-phylo-dbgsym_1.0.11-9+b1_amd64.deb: OK md5: prime-phylo_1.0.11-9+b1_amd64.deb: OK sha1: prime-phylo-dbgsym_1.0.11-9+b1_amd64.deb: OK sha1: prime-phylo_1.0.11-9+b1_amd64.deb: OK sha256: prime-phylo-dbgsym_1.0.11-9+b1_amd64.deb: OK sha256: prime-phylo_1.0.11-9+b1_amd64.deb: OK Checksums: OK