Thu Jan 23 08:29:34 UTC 2025 I: starting to build prime-phylo/trixie/amd64 on jenkins on '2025-01-23 08:29' Thu Jan 23 08:29:34 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_35/44430/console.log Thu Jan 23 08:29:34 UTC 2025 I: Downloading source for trixie/prime-phylo=1.0.11-13 --2025-01-23 08:29:34-- http://deb.debian.org/debian/pool/main/p/prime-phylo/prime-phylo_1.0.11-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2366 (2.3K) [text/prs.lines.tag] Saving to: ‘prime-phylo_1.0.11-13.dsc’ 0K .. 100% 203M=0s 2025-01-23 08:29:34 (203 MB/s) - ‘prime-phylo_1.0.11-13.dsc’ saved [2366/2366] Thu Jan 23 08:29:34 UTC 2025 I: prime-phylo_1.0.11-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prime-phylo Binary: prime-phylo Architecture: any Version: 1.0.11-13 Maintainer: Debian Med Packaging Team Uploaders: Erik Sjolund , Andreas Tille , Étienne Mollier Homepage: http://prime.sbc.su.se Standards-Version: 4.7.0 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 1b610ab09a7f030983645b55c899925f1274795b 11008 prime-phylo_1.0.11-13.debian.tar.xz Checksums-Sha256: 5d46b4e528417bb4a0be56756069f255f86ab58b28b55fa6a96983f10585bd8d 750651 prime-phylo_1.0.11.orig.tar.gz c038988e04bff12b839bb04944b83adf4f3c6fd919e3eedde830f6d8cbfdbd58 11008 prime-phylo_1.0.11-13.debian.tar.xz Files: 0356071434de01edf92a1b9182ed6ef1 750651 prime-phylo_1.0.11.orig.tar.gz 5dd29777cf77e181037010c776918890 11008 prime-phylo_1.0.11-13.debian.tar.xz Dgit: 145774abd804a6a885854671c901ccad9cc48798 debian archive/debian/1.0.11-13 https://git.dgit.debian.org/prime-phylo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcnkBIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpL1BAAp9XpiZ5LVth6Fs6LGy7LgxXJCor8 Z/tKZRfDyh1Og7tM+UW0fu+l3NdndnauNcYuLJv6Gw33ErKDlCikirk6laz9R1kw M/hjhEgv6kAFXAQPcZsMF7aBFZCVUeB/Hp4f2T8tAiyKEUgofngH/C6xeCzTUu/7 NhLKLqXfazngPYa33wUDAW0TYLN2Ntr/IIeqJivg1Xjn1RKGL1LkCHNM1SsbOiFQ h7NXhpbS+R34ka2vCNeA+effxReup8KqQ/H9S7CxFaC12Ux3ps/LCqvnWQfMbu2D PgxY1zD/cICUVFWcEQTlUZ4aMr9IokgLEoN/uGV9bBWnQ1dETDlsTqLGSYiWchvQ Hrzl52Yg3w1V04jfwkFom20G5x7+jj+BIbwrJOTOG7ha6RP7lDXzja0cw2Z8Lqm4 IxZ73OH1dBcTeXuBxXk9diWnfJOjmgdVMppEtVxr/3O9J1m4GbDLbRN75oC1kjw+ fwEx3tWo8xkHV3tweELTT7uTkmdMakmp6hFJVBcRScSCslh2RTlu7AwkJyt3MLWj bsvdrqKbDEcxw6qMmB4zEAOdeHJ1Dzrm0cAExMCz6/9qpsUtH65OOi/y1498Hdzc EcQs2TgLfNlTR9gVBmAuZNjys2wCfL8iKlZZgd6jGakQjpwpEqqQhN+45dORvEGB 09bmjkBMY24zMAY= =ilxE -----END PGP SIGNATURE----- Thu Jan 23 08:29:34 UTC 2025 I: Checking whether the package is not for us Thu Jan 23 08:29:34 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Thu Jan 23 08:29:34 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Thu Jan 23 08:32:04 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jan 22 20:29:36 -12 2025 I: pbuilder-time-stamp: 1737620976 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_1.0.11-13.dsc] I: copying [./prime-phylo_1.0.11.orig.tar.gz] I: copying [./prime-phylo_1.0.11-13.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./prime-phylo_1.0.11-13.dsc: unsupported subcommand 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_1.0.11-13.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 dpkg-source: info: applying fix-ftbfs-with-gcc13.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying openmpi5.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3224612/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e94d7679a9364c948646eea528a5d7ba' 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='3224612' 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.IJrI9x6F/pbuilderrc_UztT --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IJrI9x6F/b1 --logfile b1/build.log prime-phylo_1.0.11-13.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-30-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3224612/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: amd64 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 ... 19856 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} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} flex{a} gengetopt{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost-mpi-dev{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcbor0.10{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libidn2-0{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnsl2{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxml2-dev{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} po-debconf{a} procps{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libfl-dev libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-pil wget xauth 0 packages upgraded, 194 newly installed, 0 to remove and 0 not upgraded. Need to get 177 MB of archives. After unpacking 851 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-5 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-5 [2164 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.8-1 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-6 [257 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-5 [1971 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-5 [677 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.8-1 [9788 B] Get: 25 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.8-1 [27.9 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.4-2 [2267 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.4-2 [12.0 MB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-2 [539 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 78 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.23 [919 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 gengetopt amd64 2.23+dfsg1-1 [173 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgfortran-14-dev amd64 14.2.0-12 [881 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-12 [11.7 MB] Get: 90 http://deb.debian.org/debian trixie/main amd64 gfortran-14 amd64 14.2.0-12 [13.4 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get: 92 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get: 93 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-6 [210 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-19 [23.6 MB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 102 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-3 [510 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-4 [161 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 112 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4 [333 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4 [373 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.6-1 [652 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libopenmpi40 amd64 5.0.6-3 [2360 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83.0 amd64 1.83.0-4 [271 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libibverbs-dev amd64 52.0-2+b1 [636 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.5.4-2 [415 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libltdl-dev amd64 2.5.4-2 [165 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-4 [616 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.16.0-1 [114 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-2 [120 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-4 [468 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libpmix-dev amd64 5.0.6-1 [3962 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 5.0.6-3 [188 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 188 http://deb.debian.org/debian trixie/main amd64 libboost-mpi1.83-dev amd64 1.83.0-4 [290 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 190 http://deb.debian.org/debian trixie/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 191 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-6 [10.4 MB] Get: 192 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Fetched 177 MB in 5s (38.6 MB/s) Preconfiguring packages ... 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 ... 19856 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b4_amd64.deb ... Unpacking flex (2.6.4-8.2+b4) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.8-5_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-5) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-5_amd64.deb ... Unpacking python3.12-minimal (3.12.8-5) ... Setting up libpython3.12-minimal:amd64 (3.12.8-5) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-5) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20359 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.8-1_amd64.deb ... Unpacking python3-minimal (3.12.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Setting up libicu72:amd64 (72.1-6) ... Setting up gengetopt (2.23+dfsg1-1) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcbor0.10:amd64 (0.10.2-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libibumad3:amd64 (52.0-2+b1) ... Setting up gettext-base (0.22.5-4) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libibmad5:amd64 (52.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jan 23 08:31:12 UTC 2025. Universal Time is now: Thu Jan 23 08:31:12 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-serialization1.83.0:amd64 (1.83.0-4) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up autopoint (0.22.5-4) ... Setting up icu-devtools (72.1-6) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libltdl7:amd64 (2.5.4-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:amd64 (14.2.0-12) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up bison (2:3.8.2+dfsg-1+b2) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.6-3) ... Setting up libtasn1-6:amd64 (4.19.0-3+b3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.4-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.15.0-1+b1) ... Setting up openssl (3.4.0-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up readline-common (8.2-6) ... Setting up libicu-dev:amd64 (72.1-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libblas-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-12) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up flex (2.6.4-8.2+b4) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-4) ... Setting up libtool (2.5.4-2) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-4) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-12) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.5.4-2) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-19) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up liblapack-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libboost-serialization-dev:amd64 (1.83.0.2+b2) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libhwloc-dev:amd64 (2.11.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up gfortran-14 (14.2.0-12) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up libibverbs1:amd64 (52.0-2+b1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up ibverbs-providers:amd64 (52.0-2+b1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Setting up gfortran (4:14.2.0-1) ... 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 libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up sphinx-common (8.1.3-4) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (5.0.6-1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... 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Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libopenmpi40:amd64 (5.0.6-3) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libboost-mpi1.83.0 (1.83.0-4) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Processing triggers for libc-bin (2.40-5) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-4) ... Setting up libpmix-dev:amd64 (5.0.6-1) ... Setting up libopenmpi-dev:amd64 (5.0.6-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Setting up libboost-mpi1.83-dev (1.83.0-4) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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_1.0.11-13_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11' dh_auto_configure -- \ -Dofficial_binary_packaging=on \ -Dprime_dynamic=on \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \ -DCMAKE_BUILD_TYPE=RELEASE cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 14.2.0 -- 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 14.2.0 -- 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 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- 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/x86_64-linux-gnu/libblas.so hittade /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for Fortran cheev -- Looking for Fortran cheev - not found -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-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/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") CMake Warning (dev) at src/cxx/CMakeLists.txt:92 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.40.0") found components: mpi serialization -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14") mpilib is /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-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/reproducible-path/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 (2.8s) 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/reproducible-path/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 (0.0s) 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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11' dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/prime-phylo-1.0.11 -B/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 [ 0%] [BISON][MyParser2] Building parser with bison 3.8.2 cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/flex -o/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-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:259.1-12: warning: nonterminal useless in grammar: darwin_entry [-Wother] 259 | darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */} | ^~~~~~~~~~~~ cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 3%] 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/gbread.c.o [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_print': /build/reproducible-path/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/reproducible-path/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; | ^~~~ gb.y: In function 'add_to_seq': gb.y:403:9: warning: unused variable 'new_buf' [-Wunused-variable] seqreader.l: In function 'seq_read': seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable] /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level: /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: 'input' defined but not used [-Wunused-function] 1864 | static int input (void) | ^~~~~ /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: 'yyunput' defined but not used [-Wunused-function] 1821 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_add_comment': /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,--dependency-file=CMakeFiles/prime-phylo-sfile.dir/link.d -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 [ 5%] [BISON][MyParser] Building parser with bison 3.8.2 cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y NHXparse.y:108.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] 108 | %expect 4 | ^~~~~~~ cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o [ 11%] 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/Beep.cc.o [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o [ 11%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Hacks.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc [ 11%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print': /build/reproducible-path/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 NHXparse.y: In function 'read_tree_string': NHXparse.y:402:20: warning: passing argument 1 of 'read_from_string' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] NHXparse.y:19:36: note: expected 'char *' but argument is of type 'const char *' /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16: warning: 'input' defined but not used [-Wunused-function] 1597 | static int input (void) | ^~~~~ /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17: warning: 'yyunput' defined but not used [-Wunused-function] 1554 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function 'new_annotation': /build/reproducible-path/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); | ^ [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TimeEstimator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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) | ^ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc:4: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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; | ^~ [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6: /build/reproducible-path/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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.hh:1, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:3: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/RandomTreeGenerator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: /build/reproducible-path/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/StrStrMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc: In constructor 'beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const beep::Real&)': /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:6: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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. | ~~~~~~~~~^~~~~~~ [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)': /build/reproducible-path/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; | ^~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:55:17: note: by 'virtual beep::Probability beep::InvGaussDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:6: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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 [ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc /build/reproducible-path/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/reproducible-path/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/reproducible-path/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); | ^~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); | ^~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' 140 | virtual void init(EdgeRateModel& erm); | ^~~~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()': /build/reproducible-path/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++) | ~~^~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/reproducible-path/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$. | ^~ [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:55:17: note: by 'virtual beep::Probability beep::InvGaussDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' 54 | Probability operator()(const Real& x) const; | ^~~~~~~~ [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/reproducible-path/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. | ^~~ [ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleObserver.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: /build/reproducible-path/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$. | ^~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' 54 | Probability operator()(const Real& x) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc: In member function 'virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)': /build/reproducible-path/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; | ^~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.hh:14, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.hh:19, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function 'virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:337:27: warning: operation on 'i' may be undefined [-Wsequence-point] 337 | p[++i] = geneFams[i]->initStateProb();//updateDataProbability(); | ^~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:337:27: warning: operation on 'i' may be undefined [-Wsequence-point] /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:337:27: warning: operation on 'i' may be undefined [-Wsequence-point] [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:23:9: note: by 'beep::BirthDeathMCMC& beep::BirthDeathMCMC::operator=(const beep::BirthDeathMCMC&)' 23 | class BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: /build/reproducible-path/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /build/reproducible-path/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/vector:62, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, | ^~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()': /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable] 897 | Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first); | ^~~~~~~~ [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/reproducible-path/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; | ^~~~~~~~~~~~~~~~ [ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc /build/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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; | ^~~~~~~ [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:17:9: note: by 'beep::fastGEM_BirthDeathProbs& beep::fastGEM_BirthDeathProbs::operator=(const beep::fastGEM_BirthDeathProbs&)' 17 | class fastGEM_BirthDeathProbs : public BirthDeathProbs | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:18:9: note: by 'beep::fastGEM_BirthDeathMCMC& beep::fastGEM_BirthDeathMCMC::operator=(const beep::fastGEM_BirthDeathMCMC&)' 18 | class fastGEM_BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~~~~~~~~~ [ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:17:9: note: by 'beep::fastGEM_BirthDeathProbs& beep::fastGEM_BirthDeathProbs::operator=(const beep::fastGEM_BirthDeathProbs&)' 17 | class fastGEM_BirthDeathProbs : public BirthDeathProbs | ^~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.hh:8, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:2: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:17:9: note: by 'beep::fastGEM_BirthDeathProbs& beep::fastGEM_BirthDeathProbs::operator=(const beep::fastGEM_BirthDeathProbs&)' 17 | class fastGEM_BirthDeathProbs : public BirthDeathProbs | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.hh:17: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)': /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printSa()': /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLb()': /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLt()': /build/reproducible-path/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; | ^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.hh:6, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' [ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()': /build/reproducible-path/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(); | ^ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.hh:12, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.hh:16, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::string beep::ReconciliationTimeModel::table4os() const': /build/reproducible-path/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; | ^~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function 'const std::string beep::ReconciliationTimeSampler::table4os() const': /build/reproducible-path/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; | ^~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const std::string&)': /build/reproducible-path/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:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:20, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] 64 | virtual TreeIO& operator=(const TreeIO &io); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' 39 | HybridTreeIO& operator=(const HybridTreeIO& io); | ^~~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:22: /build/reproducible-path/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++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:11: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const': /build/reproducible-path/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) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeGenerator.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: note: by 'virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)' 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: note: by 'virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)' 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: warning: 'virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)' was hidden [-Woverloaded-virtual=] /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:22:9: note: by 'beep::BirthDeathInHybridMCMC& beep::BirthDeathInHybridMCMC::operator=(const beep::BirthDeathInHybridMCMC&)' 22 | class BirthDeathInHybridMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' [ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] 64 | virtual TreeIO& operator=(const TreeIO &io); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' 39 | HybridTreeIO& operator=(const HybridTreeIO& io); | ^~~~~~~~ [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SeqIO.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' 54 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /usr/include/c++/14/ext/hash_map:60, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: /usr/include/c++/14/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 \ | ^~~~~~~ [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | MatrixCache(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); | ^~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' 140 | virtual void init(EdgeRateModel& erm); | ^~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.hh:131:17: warning: 'virtual std::string beep::SubstitutionModel::print() const' was hidden [-Woverloaded-virtual=] 131 | std::string print() const; | ^~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:147:17: note: by 'std::string beep::FastCacheSubstitutionModel::print(bool) const' 147 | std::string print(bool estimateRates = false) const; | ^~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); | ^~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' 140 | virtual void init(EdgeRateModel& erm); | ^~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc:2: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | MatrixCache(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc [ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); | ^~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' 140 | virtual void init(EdgeRateModel& erm); | ^~~~ /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:8: /build/reproducible-path/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); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:16: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | MatrixCache(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': /build/reproducible-path/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() | ^~~~~~~~~ [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': /build/reproducible-path/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), | ^~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map beep::SequenceData::getBaseFrequencies()': /build/reproducible-path/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/reproducible-path/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++) { | ~~^~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); | ^~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' 140 | virtual void init(EdgeRateModel& erm); | ^~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: /build/reproducible-path/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. | ^~~ [ 81%] Linking CXX shared library libprime-phylo.so cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/prime-phylo.dir/link.d -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" 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"CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o" "CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o" "CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o" "CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o" "CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o" "CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o" "CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o" "CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o" "CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o" "CMakeFiles/prime-phylo.dir/HybridTree.cc.o" "CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o" "CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o" "CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o" "CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o" "CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o" "CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o" "CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o" "CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o" "CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o" "CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o" "CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o" "CMakeFiles/prime-phylo.dir/MatrixCache.cc.o" "CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o" "CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o" "CMakeFiles/prime-phylo.dir/SeqIO.cc.o" "CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o" "CMakeFiles/prime-phylo.dir/SequenceType.cc.o" "CMakeFiles/prime-phylo.dir/SequenceData.cc.o" "CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o" "CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o" "CMakeFiles/prime-phylo.dir/LA_Vector.cc.o" "CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o" "CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o" -L/usr/lib/x86_64-linux-gnu/liblapack.so -L/usr/lib/x86_64-linux-gnu/libblas.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu/liblapack.so:/usr/lib/x86_64-linux-gnu/libblas.so:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../sfile/libprime-phylo-sfile.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 81%] Built target prime-phylo make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-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 -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 82%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h [ 85%] Generating cmdline.c, cmdline.h [ 85%] Generating cmdline.c, cmdline.h [ 85%] Generating cmdline.c, cmdline.h cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 85%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o [ 85%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw 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/build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make 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/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB 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/usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize 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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.c cd 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-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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc [ 91%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c [ 92%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc [ 92%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c [ 92%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] 64 | virtual TreeIO& operator=(const TreeIO &io); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' 39 | HybridTreeIO& operator=(const HybridTreeIO& io); | ^~~~~~~~ [ 93%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c [ 93%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)': /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'int main(int, char**)': /build/reproducible-path/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/reproducible-path/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) | ^ [ 94%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.c In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc: In function 'int main(int, char**)': /build/reproducible-path/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/reproducible-path/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) { | ^ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)': /build/reproducible-path/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/reproducible-path/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) { | ^ [ 95%] Linking CXX executable showtree cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 [ 96%] Linking CXX executable treesize cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 [ 96%] Linking CXX executable tree2leafnames cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/treesize.dir/link.d CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/tree2leafnames.dir/link.d CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 96%] Built target treesize [ 96%] Built target tree2leafnames /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/showtree.dir/link.d CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 96%] Built target showtree In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); | ^~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' 140 | virtual void init(EdgeRateModel& erm); | ^~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:15: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:16: /build/reproducible-path/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$ | ^~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:55:17: note: by 'virtual beep::Probability beep::InvGaussDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:17: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:18: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | MatrixCache(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:2: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:23:9: note: by 'beep::BirthDeathMCMC& beep::BirthDeathMCMC::operator=(const beep::BirthDeathMCMC&)' 23 | class BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:27: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)': /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadHostTree(gengetopt_args_info&)': /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'int main(int, char**)': /build/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:28: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function 'int main(int, char**)': /build/reproducible-path/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) | ^ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /build/reproducible-path/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++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': /build/reproducible-path/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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:10: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh: At global scope: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); | ^~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' 140 | virtual void init(EdgeRateModel& erm); | ^~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: /build/reproducible-path/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$ | ^~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:55:17: note: by 'virtual beep::Probability beep::InvGaussDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:14: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:15: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | MatrixCache(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /build/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:27: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:28: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:14: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 30 | NodeMap(const Tree &G, const C defval); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 31 | NodeMap(const NodeMap &nm); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': /build/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': /build/reproducible-path/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:10: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:14: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)': /build/reproducible-path/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/reproducible-path/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/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1 [ 97%] Linking CXX executable chainsaw cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/primeGEM.dir/link.d CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 97%] Built target primeGEM /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/chainsaw.dir/link.d CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 97%] Built target chainsaw [ 97%] Linking CXX executable reconcile cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/reconcile.dir/link.d CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 97%] Built target reconcile [ 98%] Linking CXX executable reroot cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/reroot.dir/link.d CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 98%] Built target reroot [ 99%] Linking CXX executable primeDLRS cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1 [100%] Linking CXX executable primeDTLSR cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/primeDLRS.dir/link.d CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [100%] Built target primeDLRS /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/primeDTLSR.dir/link.d CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [100%] Built target primeDTLSR make[2]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-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-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/prime-phylo-1.0.11 -B/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Debug" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/chainsaw.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDLRS.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeGEM.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reconcile.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reroot.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/showtree.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/treesize.1 -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw -- Set non-toolchain portion of runtime path of "/build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo" -- Installing: /build/reproducible-path/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/mcmc_analysis make[1]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-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_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake debian/rules override_dh_makeshlibs make[1]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11' dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so make[1]: Leaving directory '/build/reproducible-path/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_1.0.11-13_amd64.deb'. dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-13_amd64.deb'. dpkg-genbuildinfo --build=binary -O../prime-phylo_1.0.11-13_amd64.buildinfo dpkg-genchanges --build=binary -O../prime-phylo_1.0.11-13_amd64.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/3224612 and its subdirectories I: Current time: Wed Jan 22 20:32:03 -12 2025 I: pbuilder-time-stamp: 1737621123 Thu Jan 23 08:32:04 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Thu Jan 23 08:32:04 UTC 2025 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Thu Jan 23 08:35:31 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. Thu Jan 23 08:35:32 UTC 2025 I: prime-phylo_1.0.11-13_amd64.changes: Format: 1.8 Date: Sun, 03 Nov 2024 14:11:50 +0100 Source: prime-phylo Binary: prime-phylo prime-phylo-dbgsym Architecture: amd64 Version: 1.0.11-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: prime-phylo - bayesian estimation of gene trees taking the species tree into ac Closes: 1086370 Changes: prime-phylo (1.0.11-13) unstable; urgency=medium . * openmpi5.patch: new: fix build failure with openmpi 5. (Closes: #1086370) * d/lintian-overrides: flag rpath, needed for openmpi. * d/salsa-ci.yml: disable i386 CI build. Checksums-Sha1: b8a7052de98e9a91d00dfc75e20a87977cabcee4 10069392 prime-phylo-dbgsym_1.0.11-13_amd64.deb 8496559b7b222508473c394b96360f9c84b943ef 10572 prime-phylo_1.0.11-13_amd64.buildinfo f5fa6190727c184b472a1b9b57ea4e8dec874396 843932 prime-phylo_1.0.11-13_amd64.deb Checksums-Sha256: 8d0650a6f2343d56c75c67e4e06c0fb034c93b7176597bfee2afae22b5cd2f51 10069392 prime-phylo-dbgsym_1.0.11-13_amd64.deb dac20f3dc3cb77d5b98c801b54e3482db7cfa9623172048084418e7e632fe6c0 10572 prime-phylo_1.0.11-13_amd64.buildinfo f61ff24c602006b449ba61661faadb046cb0ddbf27894182a3fe2802412a0c19 843932 prime-phylo_1.0.11-13_amd64.deb Files: c3d47625d5d500ff400bd0bc64e8039f 10069392 debug optional prime-phylo-dbgsym_1.0.11-13_amd64.deb 2149f15e476631cc6d776efb6711dd03 10572 science optional prime-phylo_1.0.11-13_amd64.buildinfo 749bd8aaf9410a2dc38aa58f12dcdc87 843932 science optional prime-phylo_1.0.11-13_amd64.deb Thu Jan 23 08:35:33 UTC 2025 I: diffoscope 285 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_35-44430.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.IJrI9x6F/prime-phylo_1.0.11-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.IJrI9x6F/prime-phylo_1.0.11-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.IJrI9x6F/prime-phylo_1.0.11-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.IJrI9x6F/b1/prime-phylo_1.0.11-13_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.IJrI9x6F/b2/prime-phylo_1.0.11-13_amd64.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: 0.453s) 0.453s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.111s) 0.111s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 786ms CPU time consumed: 786ms Thu Jan 23 08:35:35 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Thu Jan 23 08:35:35 UTC 2025 I: prime-phylo from trixie built successfully and reproducibly on amd64. Thu Jan 23 08:35:36 UTC 2025 I: Submitting .buildinfo files to external archives: Thu Jan 23 08:35:36 UTC 2025 I: Submitting 12K b1/prime-phylo_1.0.11-13_amd64.buildinfo.asc Thu Jan 23 08:35:37 UTC 2025 I: Submitting 12K b2/prime-phylo_1.0.11-13_amd64.buildinfo.asc Thu Jan 23 08:35:37 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jan 23 08:35:37 UTC 2025 I: Done submitting .buildinfo files. Thu Jan 23 08:35:37 UTC 2025 I: Removing signed prime-phylo_1.0.11-13_amd64.buildinfo.asc files: removed './b1/prime-phylo_1.0.11-13_amd64.buildinfo.asc' removed './b2/prime-phylo_1.0.11-13_amd64.buildinfo.asc'