Tue Apr 11 11:50:30 UTC 2023 I: starting to build prime-phylo/bookworm/arm64 on jenkins on '2023-04-11 11:50' Tue Apr 11 11:50:30 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/25200/console.log Tue Apr 11 11:50:30 UTC 2023 I: Downloading source for bookworm/prime-phylo=1.0.11-10 --2023-04-11 11:50:31-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/prime-phylo/prime-phylo_1.0.11-10.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2204 (2.2K) [text/prs.lines.tag] Saving to: ‘prime-phylo_1.0.11-10.dsc’ 0K .. 100% 24.1M=0s 2023-04-11 11:50:31 (24.1 MB/s) - ‘prime-phylo_1.0.11-10.dsc’ saved [2204/2204] Tue Apr 11 11:50:31 UTC 2023 I: prime-phylo_1.0.11-10.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prime-phylo Binary: prime-phylo Architecture: any Version: 1.0.11-10 Maintainer: Debian Med Packaging Team Uploaders: Erik Sjolund , Andreas Tille Homepage: http://prime.sbc.su.se Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev Package-List: prime-phylo deb science optional arch=any Checksums-Sha1: 1dd3b086599e29f6a17319f8ebe294cd6eed0c07 750651 prime-phylo_1.0.11.orig.tar.gz 1ebfeb46f30c711a7d5412fa0e1ab55c4f7f9b90 8524 prime-phylo_1.0.11-10.debian.tar.xz Checksums-Sha256: 5d46b4e528417bb4a0be56756069f255f86ab58b28b55fa6a96983f10585bd8d 750651 prime-phylo_1.0.11.orig.tar.gz e706500586da3c2d85b897a4b8c735e84777b326c26a3026de52a5597220070d 8524 prime-phylo_1.0.11-10.debian.tar.xz Files: 0356071434de01edf92a1b9182ed6ef1 750651 prime-phylo_1.0.11.orig.tar.gz 590a5f5af75916aed9f33f555173be65 8524 prime-phylo_1.0.11-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmEZIuYUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafEN6A//aiLR8Q9yQCLZcWqFnHN2MUa7u9fm qUcm31oWjMr+te/tNvrDOHzXMPR+MIIwtPh0h32SDCfbDzCyVUs/u6jqyNXmTqY9 HarNdLFzIEnHncL2Esvk4DocWWgzGctRJ+J7rWlR+2ZP+vyujzPmvFqqkVfLBjct zKU1L8RB2W7iLJk6EVB8IK+8wwOl314eGTjVS94/GmllzcHFL1M0by/2OvaRR0Bj 4gAt1vuaO1tZjduLkzgwwUCmTbSDwDfSFBvakpfNf3zi2ZW6GS2Flrx5z9nZaQIX rmWUYK82LCrs5CBZxmpUEacwokmkKin3/yS1WWZd899d77kKWzo8De9WSeO80oBX rzvaWNAX3FpCP4l+WaIRIQJlllpKYL45BQVsECS0sxM5F7MxlqocxPThDgOLiW3Q lXz2A5YyxRTsfrNJA2lO7J7mKbqfdlGeZGzihSD1X+1xOODGFoYnqhnQGOMcA5QC 7x9mNGgA3l+qfqQJopUaRDjOMEohM0b0BHTVGggUr8sggKL6tLF5ieFVwHU7jCxQ JW4RdB/3mt0akCZqShan8xeBIefR8Z0FekIfUO7BUpboseTRK+5GHbFPBA2/vHyJ LyzWwB6wf1rShAh7tnko2COG8WarbBLK+NOAQlgPluntFs1h74g0OruFKr6FHmPH Ssyvfg47vFh0G0Y= =zqz0 -----END PGP SIGNATURE----- Tue Apr 11 11:50:31 UTC 2023 I: Checking whether the package is not for us Tue Apr 11 11:50:31 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Tue Apr 11 11:50:31 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Tue Apr 11 11:55:07 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 13 06:13:33 -12 2024 I: pbuilder-time-stamp: 1715624013 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [prime-phylo_1.0.11-10.dsc] I: copying [./prime-phylo_1.0.11.orig.tar.gz] I: copying [./prime-phylo_1.0.11-10.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 15 02:21:26 2021 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./prime-phylo_1.0.11-10.dsc: no acceptable signature found dpkg-source: info: extracting prime-phylo in prime-phylo-1.0.11 dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-10.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7123/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='7123' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8INVvBiV/pbuilderrc_g7oE --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8INVvBiV/b1 --logfile b1/build.log prime-phylo_1.0.11-10.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 13 04:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/7123/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gengetopt; however: Package gengetopt is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libxml2-dev; however: Package libxml2-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-mpi-dev; however: Package libboost-mpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-serialization-dev; however: Package libboost-serialization-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bison{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} flex{a} gengetopt{a} gettext{a} gettext-base{a} gfortran{a} gfortran-12{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost-mpi-dev{a} libboost-mpi1.74-dev{a} libboost-mpi1.74.0{a} libboost-serialization-dev{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcbor0.8{a} libcurl4{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp25{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2{a} libproc2-0{a} libpsl5{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libucx0{a} libuv1{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxml2-dev{a} libxnvctrl0{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libfl-dev libldap-common libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget xauth 0 packages upgraded, 118 newly installed, 0 to remove and 0 not upgraded. Need to get 82.0 MB of archives. After unpacking 468 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 flex arm64 2.6.4-8.1 [430 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libcbor0.8 arm64 0.8.0-2+b1 [26.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 libfido2-1 arm64 1.12.0-2+b1 [72.6 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 openssh-client arm64 1:9.2p1-2 [931 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 bison arm64 2:3.8.2+dfsg-1+b1 [1152 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-7 [361 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 gengetopt arm64 2.23+dfsg1-1 [155 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libgfortran-12-dev arm64 12.2.0-14 [396 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 gfortran-12 arm64 12.2.0-14 [8646 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 gfortran arm64 4:12.2.0-3 [1420 B] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libnl-3-200 arm64 3.7.0-0.2+b1 [60.2 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-200 arm64 3.7.0-0.2+b1 [168 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libibverbs1 arm64 44.0-2 [56.8 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 ibverbs-providers arm64 44.0-2 [306 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 icu-devtools arm64 72.1-3 [192 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libblas-dev arm64 3.11.0-2 [97.6 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74.0 arm64 1.74.0+ds1-20 [308 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74-dev arm64 1.74.0+ds1-20 [357 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-8 [124 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-8 [53.7 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 librdmacm1 arm64 44.0-2 [64.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libfabric1 arm64 1.17.0-3 [476 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libhwloc15 arm64 2.9.0-1 [133 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libmunge2 arm64 0.5.15-2 [18.8 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libpciaccess0 arm64 0.17-2 [50.4 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 libxnvctrl0 arm64 525.85.05-1 [13.3 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 ocl-icd-libopencl1 arm64 2.3.1-1 [42.1 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libhwloc-plugins arm64 2.9.0-1 [17.2 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 libpmix2 arm64 4.2.2-1+b1 [554 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libnuma1 arm64 2.0.16-1 [20.3 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libucx0 arm64 1.13.1-1 [734 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libopenmpi3 arm64 4.1.4-3+b1 [2161 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi1.74.0 arm64 1.74.0+ds1-20 [254 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 openmpi-common all 4.1.4-3 [167 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libnl-3-dev arm64 3.7.0-0.2+b1 [104 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-dev arm64 3.7.0-0.2+b1 [200 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libibverbs-dev arm64 44.0-2 [613 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libnuma-dev arm64 2.0.16-1 [36.0 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libltdl7 arm64 2.4.7-5 [392 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libltdl-dev arm64 2.4.7-5 [165 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libhwloc-dev arm64 2.9.0-1 [734 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libevent-2.1-7 arm64 2.1.12-stable-8 [168 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libevent-extra-2.1-7 arm64 2.1.12-stable-8 [101 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libevent-openssl-2.1-7 arm64 2.1.12-stable-8 [59.7 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 libevent-dev arm64 2.1.12-stable-8 [302 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libpmix-dev arm64 4.2.2-1+b1 [883 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 openmpi-bin arm64 4.1.4-3+b1 [225 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libopenmpi-dev arm64 4.1.4-3+b1 [970 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 mpi-default-dev arm64 1.14 [5548 B] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi1.74-dev arm64 1.74.0+ds1-20 [277 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi-dev arm64 1.74.0.3 [4420 B] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization-dev arm64 1.74.0.3 [4560 B] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libicu-dev arm64 72.1-3 [10.2 MB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libxml2-dev arm64 2.9.14+dfsg-1.1+b3 [740 kB] Fetched 82.0 MB in 1s (55.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../000-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package flex. Preparing to unpack .../001-flex_2.6.4-8.1_arm64.deb ... Unpacking flex (2.6.4-8.1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../006-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../014-libbsd0_0.11.7-2_arm64.deb ... Unpacking libbsd0:arm64 (0.11.7-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../015-libedit2_3.1-20221030-2_arm64.deb ... Unpacking libedit2:arm64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:arm64. Preparing to unpack .../016-libcbor0.8_0.8.0-2+b1_arm64.deb ... Unpacking libcbor0.8:arm64 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../017-libfido2-1_1.12.0-2+b1_arm64.deb ... Unpacking libfido2-1:arm64 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../018-openssh-client_1%3a9.2p1-2_arm64.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../021-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../022-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package bison. Preparing to unpack .../023-bison_2%3a3.8.2+dfsg-1+b1_arm64.deb ... Unpacking bison (2:3.8.2+dfsg-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../024-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../025-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package libarchive13:arm64. Preparing to unpack .../026-libarchive13_3.6.2-1_arm64.deb ... Unpacking libarchive13:arm64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../027-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../030-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../031-libnghttp2-14_1.52.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.52.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../032-libpsl5_0.21.2-1_arm64.deb ... Unpacking libpsl5:arm64 (0.21.2-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../034-libssh2-1_1.10.0-3+b1_arm64.deb ... Unpacking libssh2-1:arm64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../035-libcurl4_7.88.1-7_arm64.deb ... Unpacking libcurl4:arm64 (7.88.1-7) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../036-libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:arm64. Preparing to unpack .../037-libjsoncpp25_1.9.5-4_arm64.deb ... Unpacking libjsoncpp25:arm64 (1.9.5-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../038-librhash0_1.4.3-3_arm64.deb ... Unpacking librhash0:arm64 (1.4.3-3) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../039-libuv1_1.44.2-1_arm64.deb ... Unpacking libuv1:arm64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../040-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../041-cmake_3.25.1-1_arm64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../046-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../047-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../048-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../049-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../050-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../052-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../053-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../054-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package gengetopt. Preparing to unpack .../055-gengetopt_2.23+dfsg1-1_arm64.deb ... Unpacking gengetopt (2.23+dfsg1-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../056-libgfortran5_12.2.0-14_arm64.deb ... Unpacking libgfortran5:arm64 (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:arm64. Preparing to unpack .../057-libgfortran-12-dev_12.2.0-14_arm64.deb ... Unpacking libgfortran-12-dev:arm64 (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../058-gfortran-12_12.2.0-14_arm64.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package gfortran. Preparing to unpack .../059-gfortran_4%3a12.2.0-3_arm64.deb ... Unpacking gfortran (4:12.2.0-3) ... Selecting previously unselected package libnl-3-200:arm64. Preparing to unpack .../060-libnl-3-200_3.7.0-0.2+b1_arm64.deb ... Unpacking libnl-3-200:arm64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:arm64. Preparing to unpack .../061-libnl-route-3-200_3.7.0-0.2+b1_arm64.deb ... Unpacking libnl-route-3-200:arm64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:arm64. Preparing to unpack .../062-libibverbs1_44.0-2_arm64.deb ... Unpacking libibverbs1:arm64 (44.0-2) ... Selecting previously unselected package ibverbs-providers:arm64. Preparing to unpack .../063-ibverbs-providers_44.0-2_arm64.deb ... Unpacking ibverbs-providers:arm64 (44.0-2) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../064-icu-devtools_72.1-3_arm64.deb ... Unpacking icu-devtools (72.1-3) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../065-libblas3_3.11.0-2_arm64.deb ... Unpacking libblas3:arm64 (3.11.0-2) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../066-libblas-dev_3.11.0-2_arm64.deb ... Unpacking libblas-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libboost1.74-dev:arm64. Preparing to unpack .../067-libboost1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../068-libboost-dev_1.74.0.3_arm64.deb ... Unpacking libboost-dev:arm64 (1.74.0.3) ... Selecting previously unselected package libboost-serialization1.74.0:arm64. Preparing to unpack .../069-libboost-serialization1.74.0_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-serialization1.74.0:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-serialization1.74-dev:arm64. Preparing to unpack .../070-libboost-serialization1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-serialization1.74-dev:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libevent-core-2.1-7:arm64. Preparing to unpack .../071-libevent-core-2.1-7_2.1.12-stable-8_arm64.deb ... Unpacking libevent-core-2.1-7:arm64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:arm64. Preparing to unpack .../072-libevent-pthreads-2.1-7_2.1.12-stable-8_arm64.deb ... Unpacking libevent-pthreads-2.1-7:arm64 (2.1.12-stable-8) ... Selecting previously unselected package librdmacm1:arm64. Preparing to unpack .../073-librdmacm1_44.0-2_arm64.deb ... Unpacking librdmacm1:arm64 (44.0-2) ... Selecting previously unselected package libfabric1:arm64. Preparing to unpack .../074-libfabric1_1.17.0-3_arm64.deb ... Unpacking libfabric1:arm64 (1.17.0-3) ... Selecting previously unselected package libhwloc15:arm64. Preparing to unpack .../075-libhwloc15_2.9.0-1_arm64.deb ... Unpacking libhwloc15:arm64 (2.9.0-1) ... Selecting previously unselected package libmunge2. Preparing to unpack .../076-libmunge2_0.5.15-2_arm64.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpciaccess0:arm64. Preparing to unpack .../077-libpciaccess0_0.17-2_arm64.deb ... Unpacking libpciaccess0:arm64 (0.17-2) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../078-libxau6_1%3a1.0.9-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../079-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../080-libxcb1_1.15-1_arm64.deb ... Unpacking libxcb1:arm64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../081-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../082-libx11-6_2%3a1.8.4-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.4-2) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../083-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:arm64. Preparing to unpack .../084-libxnvctrl0_525.85.05-1_arm64.deb ... Unpacking libxnvctrl0:arm64 (525.85.05-1) ... Selecting previously unselected package ocl-icd-libopencl1:arm64. Preparing to unpack .../085-ocl-icd-libopencl1_2.3.1-1_arm64.deb ... Unpacking ocl-icd-libopencl1:arm64 (2.3.1-1) ... Selecting previously unselected package libhwloc-plugins:arm64. Preparing to unpack .../086-libhwloc-plugins_2.9.0-1_arm64.deb ... Unpacking libhwloc-plugins:arm64 (2.9.0-1) ... Selecting previously unselected package libpmix2:arm64. Preparing to unpack .../087-libpmix2_4.2.2-1+b1_arm64.deb ... Unpacking libpmix2:arm64 (4.2.2-1+b1) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../088-libnuma1_2.0.16-1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.16-1) ... Selecting previously unselected package libucx0:arm64. Preparing to unpack .../089-libucx0_1.13.1-1_arm64.deb ... Unpacking libucx0:arm64 (1.13.1-1) ... Selecting previously unselected package libopenmpi3:arm64. Preparing to unpack .../090-libopenmpi3_4.1.4-3+b1_arm64.deb ... Unpacking libopenmpi3:arm64 (4.1.4-3+b1) ... Selecting previously unselected package libboost-mpi1.74.0. Preparing to unpack .../091-libboost-mpi1.74.0_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-mpi1.74.0 (1.74.0+ds1-20) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../092-openmpi-common_4.1.4-3_all.deb ... Unpacking openmpi-common (4.1.4-3) ... Selecting previously unselected package libnl-3-dev:arm64. Preparing to unpack .../093-libnl-3-dev_3.7.0-0.2+b1_arm64.deb ... Unpacking libnl-3-dev:arm64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-dev:arm64. Preparing to unpack .../094-libnl-route-3-dev_3.7.0-0.2+b1_arm64.deb ... Unpacking libnl-route-3-dev:arm64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs-dev:arm64. Preparing to unpack .../095-libibverbs-dev_44.0-2_arm64.deb ... Unpacking libibverbs-dev:arm64 (44.0-2) ... Selecting previously unselected package libnuma-dev:arm64. Preparing to unpack .../096-libnuma-dev_2.0.16-1_arm64.deb ... Unpacking libnuma-dev:arm64 (2.0.16-1) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../097-libltdl7_2.4.7-5_arm64.deb ... Unpacking libltdl7:arm64 (2.4.7-5) ... Selecting previously unselected package libltdl-dev:arm64. Preparing to unpack .../098-libltdl-dev_2.4.7-5_arm64.deb ... Unpacking libltdl-dev:arm64 (2.4.7-5) ... Selecting previously unselected package libhwloc-dev:arm64. Preparing to unpack .../099-libhwloc-dev_2.9.0-1_arm64.deb ... Unpacking libhwloc-dev:arm64 (2.9.0-1) ... Selecting previously unselected package libevent-2.1-7:arm64. Preparing to unpack .../100-libevent-2.1-7_2.1.12-stable-8_arm64.deb ... Unpacking libevent-2.1-7:arm64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:arm64. Preparing to unpack .../101-libevent-extra-2.1-7_2.1.12-stable-8_arm64.deb ... Unpacking libevent-extra-2.1-7:arm64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:arm64. Preparing to unpack .../102-libevent-openssl-2.1-7_2.1.12-stable-8_arm64.deb ... Unpacking libevent-openssl-2.1-7:arm64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../103-libevent-dev_2.1.12-stable-8_arm64.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../104-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpmix-dev:arm64. Preparing to unpack .../105-libpmix-dev_4.2.2-1+b1_arm64.deb ... Unpacking libpmix-dev:arm64 (4.2.2-1+b1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../106-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../107-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../108-openmpi-bin_4.1.4-3+b1_arm64.deb ... Unpacking openmpi-bin (4.1.4-3+b1) ... Selecting previously unselected package libopenmpi-dev:arm64. Preparing to unpack .../109-libopenmpi-dev_4.1.4-3+b1_arm64.deb ... Unpacking libopenmpi-dev:arm64 (4.1.4-3+b1) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../110-mpi-default-dev_1.14_arm64.deb ... Unpacking mpi-default-dev (1.14) ... Selecting previously unselected package libboost-mpi1.74-dev. Preparing to unpack .../111-libboost-mpi1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-mpi1.74-dev (1.74.0+ds1-20) ... Selecting previously unselected package libboost-mpi-dev. Preparing to unpack .../112-libboost-mpi-dev_1.74.0.3_arm64.deb ... Unpacking libboost-mpi-dev (1.74.0.3) ... Selecting previously unselected package libboost-serialization-dev:arm64. Preparing to unpack .../113-libboost-serialization-dev_1.74.0.3_arm64.deb ... Unpacking libboost-serialization-dev:arm64 (1.74.0.3) ... Selecting previously unselected package libicu-dev:arm64. Preparing to unpack .../114-libicu-dev_72.1-3_arm64.deb ... Unpacking libicu-dev:arm64 (72.1-3) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../115-liblapack3_3.11.0-2_arm64.deb ... Unpacking liblapack3:arm64 (3.11.0-2) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../116-liblapack-dev_3.11.0-2_arm64.deb ... Unpacking liblapack-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libxml2-dev:arm64. Preparing to unpack .../117-libxml2-dev_2.9.14+dfsg-1.1+b3_arm64.deb ... Unpacking libxml2-dev:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libpciaccess0:arm64 (0.17-2) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libicu72:arm64 (72.1-3) ... Setting up gengetopt (2.23+dfsg1-1) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libcbor0.8:arm64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libuv1:arm64 (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:arm64 (2:4.0.2-3) ... Setting up libhwloc15:arm64 (2.9.0-1) ... Setting up libevent-core-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libevent-2.1-7:arm64 (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:arm64 (1.9.5-4) ... Setting up icu-devtools (72.1-3) ... Setting up libltdl7:arm64 (2.4.7-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libboost-serialization1.74.0:arm64 (1.74.0+ds1-20) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up libnuma1:arm64 (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:arm64 (2.3.1-1) ... Setting up librhash0:arm64 (1.4.3-3) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libnl-3-200:arm64 (3.7.0-0.2+b1) ... Setting up bison (2:3.8.2+dfsg-1+b1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:arm64 (1.12.0-2+b1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libicu-dev:arm64 (72.1-3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libblas-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-8) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:arm64 (2.1.12-stable-8) ... Setting up flex (2.6.4-8.1) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:arm64 (3.6.2-1) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libevent-openssl-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libgfortran-12-dev:arm64 (12.2.0-14) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.16-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-5) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libxml2-dev:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up liblapack-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libboost-serialization1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:arm64 (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:arm64 (7.88.1-7) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libhwloc-dev:arm64 (2.9.0-1) ... Setting up libibverbs1:arm64 (44.0-2) ... Setting up ibverbs-providers:arm64 (44.0-2) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:12.2.0-3) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libxnvctrl0:arm64 (525.85.05-1) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.2+b1) ... Setting up libboost-serialization-dev:arm64 (1.74.0.3) ... Setting up cmake (3.25.1-1) ... Setting up librdmacm1:arm64 (44.0-2) ... Setting up libucx0:arm64 (1.13.1-1) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:arm64 (44.0-2) ... Setting up libhwloc-plugins:arm64 (2.9.0-1) ... Setting up libfabric1:arm64 (1.17.0-3) ... Setting up libpmix2:arm64 (4.2.2-1+b1) ... Setting up libopenmpi3:arm64 (4.1.4-3+b1) ... Setting up libboost-mpi1.74.0 (1.74.0+ds1-20) ... Setting up libpmix-dev:arm64 (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:arm64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.14) ... Setting up libboost-mpi1.74-dev (1.74.0+ds1-20) ... Setting up libboost-mpi-dev (1.74.0.3) ... Processing triggers for libc-bin (2.36-8) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/prime-phylo-1.0.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../prime-phylo_1.0.11-10_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 dh binary --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/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-aarch64-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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 12.2.0 -- 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 12.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- The C compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so hittade /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for Fortran cheev -- Looking for Fortran cheev - not found -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Found BISON: /usr/bin/bison (found version "3.8.2") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI_Fortran: /usr/lib/aarch64-linux-gnu/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Found Boost: /usr/lib/aarch64-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/aarch64-linux-gnu/libxml2.so (found version "2.9.14") mpilib is /usr/lib/aarch64-linux-gnu/openmpi/include;/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi 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-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 CMake Warning (dev) at src/cxx/tools/tree2leafnames/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/prime-phylo-1.0.11' dh_auto_build -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-1.0.11 -B/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/CMakeFiles /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu' [ 1%] [BISON][MyParser2] Building parser with bison 3.8.2 [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 cd /build/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/flex -o/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l cd /build/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y 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-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/libraries/sfile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu' [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -MF CMakeFiles/prime-phylo-sfile.dir/sfile.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gbread.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -MF CMakeFiles/prime-phylo-sfile.dir/lexer.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c: In function 'main': /build/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-1.0.11/src/cxx/libraries/sfile/gbread.c:8:1: note: include '' or provide a declaration of 'strcmp' 7 | #include "gb.tab.h" +++ |+#include 8 | /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_print': /build/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-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c: In function 'yyparse': /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1096:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration] 1096 | 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] /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level: /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-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 ) | ^~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_add_comment': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:303:20: warning: array subscript 'struct comment[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 303 | tmp->text = strdup(s); | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by 'malloc' 301 | tmp = (struct comment *) malloc(sizeof(struct comment *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:304:20: warning: array subscript 'struct comment[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds] 304 | tmp->next = NULL; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by 'malloc' 301 | tmp = (struct comment *) malloc(sizeof(struct comment *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 4%] Linking C shared library libprime-phylo-sfile.so cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu' [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 [ 5%] [BISON][MyParser] Building parser with bison 3.8.2 cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/prime-phylo-1.0.11/obj-aarch64-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 | ^~~~~~~ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/libraries/prime /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu' [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -MF CMakeFiles/prime-phylo.dir/NHXtree.c.o.d -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -MF CMakeFiles/prime-phylo.dir/NHXannotation.c.o.d -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -MF CMakeFiles/prime-phylo.dir/NHXparse.c.o.d -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -MF CMakeFiles/prime-phylo.dir/AnError.cc.o.d -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o -MF CMakeFiles/prime-phylo.dir/BeepOption.cc.o.d -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o -MF CMakeFiles/prime-phylo.dir/Beep.cc.o.d -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c:155:32: 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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c: In function 'yytree_parse': /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:1112:16: note: in expansion of macro 'yylex' 1112 | yychar = yylex (); | ^~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function 'new_annotation': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c:80:3: warning: '__builtin_strncpy' specified bound 5 equals destination size [-Wstringop-truncation] 80 | strncpy(a->anno_type, tag, MAX_ANNOTATION_ID_LENGTH); | ^ 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] [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o -MF CMakeFiles/prime-phylo.dir/Hacks.cc.o.d -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Hacks.cc /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-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 ) | ^~~~~~~ [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o -MF CMakeFiles/prime-phylo.dir/PRNG.cc.o.d -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.cc cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o -MF CMakeFiles/prime-phylo.dir/ODESolver.cc.o.d -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -MF CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o.d -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -MF CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc: In member function 'std::pair beep::option::BeepOptionMap::getDoubleX2(std::string)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:592:59: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 592 | pair BeepOptionMap::getDoubleX2(string name) | ^ [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -MF CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -MF CMakeFiles/prime-phylo.dir/Probability.cc.o.d -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc:4: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C3' of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C4' of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C5' of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A21' of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A31' of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A32' of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A41' of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A42' of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A43' of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A51' of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A52' of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/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 beep::Real beep::ODESolver::A53' of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A54' of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/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 beep::Real beep::ODESolver::A61' of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/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 beep::Real beep::ODESolver::A62' of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/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 beep::Real beep::ODESolver::A63' of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/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 beep::Real beep::ODESolver::A64' of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/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 beep::Real beep::ODESolver::A65' of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/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 beep::Real beep::ODESolver::A71' of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/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 beep::Real beep::ODESolver::A73' of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/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 beep::Real beep::ODESolver::A74' of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/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 beep::Real beep::ODESolver::A75' of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/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 beep::Real beep::ODESolver::A76' of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/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 beep::Real beep::ODESolver::E1' of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/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 beep::Real beep::ODESolver::E3' of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/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 beep::Real beep::ODESolver::E4' of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/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 beep::Real beep::ODESolver::E5' of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/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 beep::Real beep::ODESolver::E6' of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/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 beep::Real beep::ODESolver::E7' of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/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 beep::Real beep::ODESolver::D1' of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/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 beep::Real beep::ODESolver::D3' of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/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 beep::Real beep::ODESolver::D4' of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/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 beep::Real beep::ODESolver::D5' of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/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 beep::Real beep::ODESolver::D6' of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/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 beep::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-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /build/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-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 405 | catch(std::exception e) | ^ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 423 | catch(std::exception e) | ^ [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -MF CMakeFiles/prime-phylo.dir/Tokenizer.cc.o.d -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -MF CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o.d -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/DiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscTree.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o -MF CMakeFiles/prime-phylo.dir/EpochTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.hh:1, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:3: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -MF CMakeFiles/prime-phylo.dir/InvMRCA.cc.o.d -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvMRCA.cc [ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o -MF CMakeFiles/prime-phylo.dir/Node.cc.o.d -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::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-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -MF CMakeFiles/prime-phylo.dir/StrStrMap.cc.o.d -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o -MF CMakeFiles/prime-phylo.dir/Tree.cc.o.d -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -MF CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -MF CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -MF CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o.d -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc: In constructor 'beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const beep::Real&)': /build/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-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:6, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:1: /build/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-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), | ^~~~ /build/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-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), | ^~~~ /build/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. | ~~~~~~~~~^~~~~~~ [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_common.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:118:29: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] 118 | buf[ bytes_read ]=NULL; | ^~~~ [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: /build/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-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:6: /build/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 beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ /build/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-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:29: warning: 'idInt' may be used uninitialized [-Wmaybe-uninitialized] 1049 | new_node = S.addNode(l, r, idInt, name); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:959:9: note: 'idInt' was declared here 959 | int idInt; | ^~~~~ [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -MF CMakeFiles/prime-phylo.dir/GammaDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc /build/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-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-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable 'rparam' [-Wunused-variable] 105 | Real rparam = variance * (rtime + ltime); | ^~~~~~ [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -MF CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -MF CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()': /build/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++) | ~~^~~~~~~~~~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -MF CMakeFiles/prime-phylo.dir/NormalDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/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$ | ^~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -MF CMakeFiles/prime-phylo.dir/UniformDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/VarRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/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 beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -MF CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCModel.cc [ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCObject.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/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 beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleML.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: /build/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 beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:6: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc /build/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-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; | ^~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -MF CMakeFiles/prime-phylo.dir/MultiGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -MF CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.cc [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc /build/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-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:27: warning: operation on 'i' may be undefined [-Wsequence-point] 338 | p[++i] = geneFams[i]->initStateProb();//updateDataProbability(); | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:27: warning: operation on 'i' may be undefined [-Wsequence-point] /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:27: warning: operation on 'i' may be undefined [-Wsequence-point] [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -MF CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C3' of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C4' of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C5' of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A21' of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A31' of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A32' of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A41' of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A42' of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A43' of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A51' of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A52' of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/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 beep::Real beep::ODESolver::A53' of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A54' of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/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 beep::Real beep::ODESolver::A61' of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/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 beep::Real beep::ODESolver::A62' of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/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 beep::Real beep::ODESolver::A63' of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/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 beep::Real beep::ODESolver::A64' of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/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 beep::Real beep::ODESolver::A65' of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/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 beep::Real beep::ODESolver::A71' of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/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 beep::Real beep::ODESolver::A73' of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/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 beep::Real beep::ODESolver::A74' of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/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 beep::Real beep::ODESolver::A75' of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/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 beep::Real beep::ODESolver::A76' of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/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 beep::Real beep::ODESolver::E1' of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/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 beep::Real beep::ODESolver::E3' of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/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 beep::Real beep::ODESolver::E4' of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/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 beep::Real beep::ODESolver::E5' of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/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 beep::Real beep::ODESolver::E6' of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/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 beep::Real beep::ODESolver::E7' of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/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 beep::Real beep::ODESolver::D1' of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/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 beep::Real beep::ODESolver::D3' of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/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 beep::Real beep::ODESolver::D4' of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/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 beep::Real beep::ODESolver::D5' of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/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 beep::Real beep::ODESolver::D6' of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/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 beep::Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -MF CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o -MF CMakeFiles/prime-phylo.dir/GammaMap.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/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-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-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-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, | ^~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()': /build/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-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-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-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-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)': /build/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); | ^~~~~~~~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ [ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C3' of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C4' of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C5' of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A21' of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A31' of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A32' of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A41' of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A42' of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A43' of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A51' of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A52' of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/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 beep::Real beep::ODESolver::A53' of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A54' of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/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 beep::Real beep::ODESolver::A61' of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/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 beep::Real beep::ODESolver::A62' of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/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 beep::Real beep::ODESolver::A63' of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/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 beep::Real beep::ODESolver::A64' of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/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 beep::Real beep::ODESolver::A65' of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/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 beep::Real beep::ODESolver::A71' of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/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 beep::Real beep::ODESolver::A73' of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/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 beep::Real beep::ODESolver::A74' of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/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 beep::Real beep::ODESolver::A75' of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/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 beep::Real beep::ODESolver::A76' of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/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 beep::Real beep::ODESolver::E1' of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/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 beep::Real beep::ODESolver::E3' of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/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 beep::Real beep::ODESolver::E4' of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/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 beep::Real beep::ODESolver::E5' of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/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 beep::Real beep::ODESolver::E6' of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/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 beep::Real beep::ODESolver::E7' of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/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 beep::Real beep::ODESolver::D1' of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/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 beep::Real beep::ODESolver::D3' of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/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 beep::Real beep::ODESolver::D4' of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/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 beep::Real beep::ODESolver::D5' of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/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 beep::Real beep::ODESolver::D6' of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/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 beep::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-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C3' of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C4' of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C5' of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A21' of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A31' of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A32' of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A41' of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A42' of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A43' of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A51' of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A52' of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/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 beep::Real beep::ODESolver::A53' of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A54' of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/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 beep::Real beep::ODESolver::A61' of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/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 beep::Real beep::ODESolver::A62' of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/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 beep::Real beep::ODESolver::A63' of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/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 beep::Real beep::ODESolver::A64' of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/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 beep::Real beep::ODESolver::A65' of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/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 beep::Real beep::ODESolver::A71' of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/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 beep::Real beep::ODESolver::A73' of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/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 beep::Real beep::ODESolver::A74' of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/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 beep::Real beep::ODESolver::A75' of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/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 beep::Real beep::ODESolver::A76' of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/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 beep::Real beep::ODESolver::E1' of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/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 beep::Real beep::ODESolver::E3' of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/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 beep::Real beep::ODESolver::E4' of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/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 beep::Real beep::ODESolver::E5' of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/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 beep::Real beep::ODESolver::E6' of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/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 beep::Real beep::ODESolver::E7' of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/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 beep::Real beep::ODESolver::D1' of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/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 beep::Real beep::ODESolver::D3' of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/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 beep::Real beep::ODESolver::D4' of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/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 beep::Real beep::ODESolver::D5' of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/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 beep::Real beep::ODESolver::D6' of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/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 beep::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-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -MF CMakeFiles/prime-phylo.dir/LambdaMap.cc.o.d -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc [ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -MF CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o.d -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:136:21: warning: variable 'topRateProb' set but not used [-Wunused-but-set-variable] 136 | Probability topRateProb = df->operator()(rate); | ^~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printSa()': /build/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-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLb()': /build/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-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLt()': /build/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; | ^~~~~~~~~~~~~~~~~ [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /build/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 beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()': /build/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(); | ^ [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -MF CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o.d -o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -MF CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o.d -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::string beep::ReconciliationTimeModel::table4os() const': /build/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; | ^~~~~~~ [ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTree.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function 'const std::string beep::ReconciliationTimeSampler::table4os() const': /build/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; | ^~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const std::string&)': /build/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:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:22, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:11: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const': /build/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) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc In file included from /usr/include/c++/12/ext/hash_map:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: /usr/include/c++/12/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixCache.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: /build/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 beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /build/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 beep::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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o -MF CMakeFiles/prime-phylo.dir/SeqIO.cc.o.d -o CMakeFiles/prime-phylo.dir/SeqIO.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /build/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 beep::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/SequenceType.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceType.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceData.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /build/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-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: /build/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 beep::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-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const SequenceType&)' has not been declared within 'beep' 270 | ostream& beep::operator<<(ostream& os, const SequenceType& dt) | ^~~~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:8: /build/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); | ^~~~~~~~ [ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Vector.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: /build/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 beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -MF CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map beep::SequenceData::getBaseFrequencies()': /build/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-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++) { | ~~^~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': /build/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-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:20:13: warning: '*this.beep::LA_Matrix::dim' is used uninitialized [-Wuninitialized] 20 | : dim(dim), | ^~~ [ 81%] Linking CXX shared library libprime-phylo.so cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 -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/aarch64-linux-gnu/liblapack.so -L/usr/lib/aarch64-linux-gnu/libblas.so -Wl,-rpath,/usr/lib/aarch64-linux-gnu/liblapack.so:/usr/lib/aarch64-linux-gnu/libblas.so:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../sfile/libprime-phylo-sfile.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-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 -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend 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-1.0.11/obj-aarch64-linux-gnu' 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-1.0.11/obj-aarch64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= 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-1.0.11/obj-aarch64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color= 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-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 83%] Generating cmdline.c, cmdline.h [ 83%] Generating cmdline.c, cmdline.h [ 83%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot 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-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 85%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize [ 85%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames [ 85%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake --color= [ 85%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -MF CMakeFiles/primeDTLSR.dir/idolatrous.cc.o.d -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -MF CMakeFiles/primeDLRS.dir/primeDLRS.cc.o.d -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build 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-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu' [ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o [ 86%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o -MF CMakeFiles/showtree.dir/showtree.cc.o.d -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o -MF CMakeFiles/reroot.dir/reroot.cc.o.d -o CMakeFiles/reroot.dir/reroot.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc 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-1.0.11/obj-aarch64-linux-gnu' [ 87%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o [ 87%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o -MF CMakeFiles/reconcile.dir/Rootalyzer.cc.o.d -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o -MF CMakeFiles/primeGEM.dir/troyo.cc.o.d -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc [ 87%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o -MF CMakeFiles/treesize.dir/treesize.cc.o.d -o CMakeFiles/treesize.dir/treesize.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc [ 88%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -MF CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o.d -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc /build/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-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-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:174:44: 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-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) | ^ /build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc: In function 'int main(int, char**)': /build/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-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)': /build/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-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) { | ^ /build/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) { | ^ [ 88%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o -MF CMakeFiles/showtree.dir/cmdline.c.o.d -o CMakeFiles/showtree.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/cmdline.c [ 89%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o -MF CMakeFiles/treesize.dir/cmdline.c.o.d -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.c [ 90%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -MF CMakeFiles/tree2leafnames.dir/cmdline.c.o.d -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c [ 90%] Linking CXX executable tree2leafnames cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 [ 91%] Linking CXX executable treesize cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/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 CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so [ 92%] Linking CXX executable showtree cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 92%] Built target tree2leafnames 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-1.0.11/obj-aarch64-linux-gnu' [ 92%] Built target treesize [ 92%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 93%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -MF CMakeFiles/primeGEM.dir/cmdline.c.o.d -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c [ 93%] Built target showtree cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color= [ 93%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -MF CMakeFiles/reconcile.dir/reconcile.cc.o.d -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu' [ 94%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o -MF CMakeFiles/chainsaw.dir/chainsaw.cc.o.d -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc [ 94%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o -MF CMakeFiles/chainsaw.dir/cmdline.c.o.d -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::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-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.hh:4, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C3' of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C4' of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C5' of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A21' of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A31' of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A32' of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A41' of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A42' of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A43' of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::A51' of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A52' of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/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 beep::Real beep::ODESolver::A53' of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/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 beep::Real beep::ODESolver::A54' of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/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 beep::Real beep::ODESolver::A61' of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/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 beep::Real beep::ODESolver::A62' of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/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 beep::Real beep::ODESolver::A63' of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/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 beep::Real beep::ODESolver::A64' of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/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 beep::Real beep::ODESolver::A65' of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/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 beep::Real beep::ODESolver::A71' of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/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 beep::Real beep::ODESolver::A73' of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/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 beep::Real beep::ODESolver::A74' of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/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 beep::Real beep::ODESolver::A75' of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/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 beep::Real beep::ODESolver::A76' of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/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 beep::Real beep::ODESolver::E1' of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/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 beep::Real beep::ODESolver::E3' of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/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 beep::Real beep::ODESolver::E4' of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/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 beep::Real beep::ODESolver::E5' of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/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 beep::Real beep::ODESolver::E6' of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/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 beep::Real beep::ODESolver::E7' of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/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 beep::Real beep::ODESolver::D1' of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/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 beep::Real beep::ODESolver::D3' of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/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 beep::Real beep::ODESolver::D4' of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/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 beep::Real beep::ODESolver::D5' of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/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 beep::Real beep::ODESolver::D6' of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/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 beep::Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::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-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:16: /build/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-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:17: /build/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 beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh: At global scope: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:14: /build/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 beep::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-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /build/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 beep::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-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: /build/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 beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 95%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o -MF CMakeFiles/reconcile.dir/cmdline.c.o.d -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/cmdline.c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:25: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 197 | catch(AnError e) | ^ [ 96%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-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-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o -MF CMakeFiles/reroot.dir/cmdline.c.o.d -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.c /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:101:65: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 101 | pair bdr = Options.getDoubleX2("BDRates"); | ^ /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:172:91: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 172 | pair edgeRateMeanVar = Options.getDoubleX2("EdgeRateParams"); | ^ /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)': /build/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-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) { | ^ [ 96%] Linking CXX executable primeGEM cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 96%] Built target primeGEM /build/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-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-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadHostTree(gengetopt_args_info&)': /build/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-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:163:24: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 163 | catch (AnError e) { | ^ /build/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) { | ^ /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': /build/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-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) { | ^ /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': /build/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 97%] Linking CXX executable chainsaw cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so [ 98%] Linking CXX executable reroot cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 98%] Built target chainsaw make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 98%] Built target reroot [ 98%] Linking CXX executable reconcile cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 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-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 98%] Built target reconcile [ 99%] Linking CXX executable primeDLRS cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 99%] Built target primeDLRS [100%] Linking CXX executable primeDTLSR cd /build/prime-phylo-1.0.11/obj-aarch64-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 -ffile-prefix-map=/build/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 CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [100%] Built target primeDTLSR make[2]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' dh_auto_test -O--buildsystem=cmake create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install --destdir=debian/prime-phylo/ -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/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-1.0.11/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-1.0.11 -B/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Debug" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/chainsaw.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDLRS.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeGEM.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reconcile.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reroot.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/showtree.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/treesize.1 -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so -- Set runtime path of "/build/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-1.0.11/debian/prime-phylo/usr/bin/primeGEM -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw -- Set runtime path of "/build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/mcmc_analysis make[1]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installexamples -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake debian/rules override_dh_makeshlibs make[1]: Entering directory '/build/prime-phylo-1.0.11' dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so make[1]: Leaving directory '/build/prime-phylo-1.0.11' dh_shlibdeps -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-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-10_arm64.deb'. dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-10_arm64.deb'. dpkg-genbuildinfo --build=binary -O../prime-phylo_1.0.11-10_arm64.buildinfo dpkg-genchanges --build=binary -O../prime-phylo_1.0.11-10_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/7123 and its subdirectories I: Current time: Mon May 13 06:18:04 -12 2024 I: pbuilder-time-stamp: 1715624284 Tue Apr 11 11:55:08 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Tue Apr 11 11:55:08 UTC 2023 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Tue Apr 11 12:14:48 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Tue Apr 11 12:14:49 UTC 2023 I: prime-phylo_1.0.11-10_arm64.changes: Format: 1.8 Date: Sun, 15 Aug 2021 19:41:37 +0530 Source: prime-phylo Binary: prime-phylo prime-phylo-dbgsym Architecture: arm64 Version: 1.0.11-10 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: prime-phylo - bayesian estimation of gene trees taking the species tree into ac Changes: prime-phylo (1.0.11-10) unstable; urgency=medium . * Team Upload. [ Shruti Sridhar ] * Add test data * Add autopkgtests * Install README as docs . [ Nilesh Patra ] * Add d/salsa-ci.yml * Bump Standards-Version to 4.5.1 (no changes needed) Checksums-Sha1: e59be5d9c54fe951e15024fc3e3deeecc333a4f3 9880204 prime-phylo-dbgsym_1.0.11-10_arm64.deb 650f61499153479528fdcbee45ea1d6843847385 8171 prime-phylo_1.0.11-10_arm64.buildinfo 1758c1c9954c92c9fab3af123029f89bee08fd2f 740668 prime-phylo_1.0.11-10_arm64.deb Checksums-Sha256: 9e43f0f4ff8dbfb0480e9a13edd27770c72ba0fd41c55e8101ffa08f3c5afe94 9880204 prime-phylo-dbgsym_1.0.11-10_arm64.deb ca0d867a734c2e6cd570fe4fa6944fa73e14bfc0016141c8b4b9162a327dd3e0 8171 prime-phylo_1.0.11-10_arm64.buildinfo b60aeadd76188d9597a093b4ef55f1c08d7487b6b59ff58a5b95e39468e51b6c 740668 prime-phylo_1.0.11-10_arm64.deb Files: f187eb03faa3448fc00305b31b94bb84 9880204 debug optional prime-phylo-dbgsym_1.0.11-10_arm64.deb 70a02199fb66498751fe75ba514c6dae 8171 science optional prime-phylo_1.0.11-10_arm64.buildinfo c17d255cf48c26711e37dd59ba5afc04 740668 science optional prime-phylo_1.0.11-10_arm64.deb Tue Apr 11 12:14:50 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8INVvBiV/prime-phylo_1.0.11-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8INVvBiV/prime-phylo_1.0.11-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8INVvBiV/prime-phylo_1.0.11-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8INVvBiV/b1/prime-phylo_1.0.11-10_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8INVvBiV/b2/prime-phylo_1.0.11-10_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.457s) 0.457s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.137s) 0.137s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue Apr 11 12:14:51 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 11 12:14:51 UTC 2023 I: prime-phylo from bookworm built successfully and reproducibly on arm64. Tue Apr 11 12:14:52 UTC 2023 I: Submitting .buildinfo files to external archives: Tue Apr 11 12:14:52 UTC 2023 I: Submitting 12K b1/prime-phylo_1.0.11-10_arm64.buildinfo.asc Tue Apr 11 12:14:53 UTC 2023 I: Submitting 12K b2/prime-phylo_1.0.11-10_arm64.buildinfo.asc Tue Apr 11 12:14:54 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 11 12:14:54 UTC 2023 I: Done submitting .buildinfo files. Tue Apr 11 12:14:54 UTC 2023 I: Removing signed prime-phylo_1.0.11-10_arm64.buildinfo.asc files: removed './b1/prime-phylo_1.0.11-10_arm64.buildinfo.asc' removed './b2/prime-phylo_1.0.11-10_arm64.buildinfo.asc'