Sun Oct 19 22:05:42 UTC 2025 I: starting to build prime-phylo/forky/amd64 on jenkins on '2025-10-19 22:05' Sun Oct 19 22:05:42 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/75726/console.log Sun Oct 19 22:05:42 UTC 2025 I: Downloading source for forky/prime-phylo=1.0.11-14 --2025-10-19 22:05:42-- http://deb.debian.org/debian/pool/main/p/prime-phylo/prime-phylo_1.0.11-14.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_1.0.11-14.dsc’ 0K .. 100% 272M=0s 2025-10-19 22:05:42 (272 MB/s) - ‘prime-phylo_1.0.11-14.dsc’ saved [2366/2366] Sun Oct 19 22:05:42 UTC 2025 I: prime-phylo_1.0.11-14.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prime-phylo Binary: prime-phylo Architecture: any Version: 1.0.11-14 Maintainer: Debian Med Packaging Team Uploaders: Erik Sjolund , Andreas Tille , Étienne Mollier Homepage: http://prime.sbc.su.se Standards-Version: 4.7.2 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 b8326a68e71693ad10cc837354f99cf221ab06ca 11760 prime-phylo_1.0.11-14.debian.tar.xz Checksums-Sha256: 5d46b4e528417bb4a0be56756069f255f86ab58b28b55fa6a96983f10585bd8d 750651 prime-phylo_1.0.11.orig.tar.gz a04cc5fe6f55536ac181904cbb0bba934c0dec125a4ebf3d2affcd5a65b42647 11760 prime-phylo_1.0.11-14.debian.tar.xz Files: 0356071434de01edf92a1b9182ed6ef1 750651 prime-phylo_1.0.11.orig.tar.gz 54305fccaa20abf04f51a910774f38bf 11760 prime-phylo_1.0.11-14.debian.tar.xz Dgit: 9132334739cc6521dd131fc532c93e06f277487c debian archive/debian/1.0.11-14 https://git.dgit.debian.org/prime-phylo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmjRqo4UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrWKg/5AX5J1t72FB8u9G3lSoatmiBdj9Fq zUiUJDSZsTGk9EX+ShTLZTIGhbWo+hR2xfmvGrZbv0ASAhESGsIC05FL0BW4TOsK OB+hGPebjpuoX3fSpfjcJT0FIa8B3bb7G+h/wJZ8p97U1bEOcvqdR4YR2U7xNm4s U4B1mwL+xDSmjE5ZlrofJvT9SSTQ/Nj59Xhsnta9WzUM0O8/E2LR6Xd5RptVWhUO Dx0rCUBYZNc1r0DDeDJSSyagRUkHVhvfLAorwUtmAGkovE4hoAVuZLt+evxzgH4a sGeCiVWc9/ldOgBatJ2Ehj42XhJIBchY3KjcqrTBc02r5Z2MEbp5y5mEp5wCcwM8 4aREKW8OhROaiJpsqMKEARVyiMvlGPhQ8lb0gaTiDMZ8s4klDPm2H7TnQfL0na8G TEavvxCUo8wU3NSZBQ/onSTiiMyaEyiWBiKzWGkdAv4PsWWO+N52O7PNh1WssoAY iAFFAEDJ0TuYwC3sbDCoxY9WgE8Lk7DwY/IF+PZZ83zNgcswXfSopTPlNeyQRBZs pWATBbYOR6S9CBQD0BOyBRkcCPzsIMvddDh3b7oeW6ZDTSJ3BqNprPbN0EpVWcd8 8ZEzVvODBT4HUZjvdQ8z1M3RWGLOleF1sA1A80qid1CFU7aBgyHC0xANBOimXowI YT+rPpcDz1oaV80= =4emy -----END PGP SIGNATURE----- Sun Oct 19 22:05:42 UTC 2025 I: Checking whether the package is not for us Sun Oct 19 22:05:42 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun Oct 19 22:05:42 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun Oct 19 22:08:55 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 19 10:05:46 -12 2025 I: pbuilder-time-stamp: 1760911546 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_1.0.11-14.dsc] I: copying [./prime-phylo_1.0.11.orig.tar.gz] I: copying [./prime-phylo_1.0.11-14.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./prime-phylo_1.0.11-14.dsc: no acceptable signature found dpkg-source: info: extracting prime-phylo in prime-phylo-1.0.11 dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-14.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 dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying cmake-4.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3674162/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=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c0c0413bf87947439e308ea1af7a12b7' 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='3674162' 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.qsySVxRZ/pbuilderrc_wbqC --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qsySVxRZ/b1 --logfile b1/build.log prime-phylo_1.0.11-14.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3674162/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 ... 19898 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gengetopt; however: Package gengetopt is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libxml2-dev; however: Package libxml2-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-mpi-dev; however: Package libboost-mpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-serialization-dev; however: Package libboost-serialization-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bison{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} flex{a} gcc-14-base{a} gengetopt{a} gettext{a} gettext-base{a} gfortran{a} gfortran-15{a} gfortran-15-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{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} libgcc-14-dev{a} libgfortran-15-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} libidn2-0{a} libjs-jquery{a} libjs-jquery-ui{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} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-ossl0{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpciaccess0{a} libpipeline1{a} libpmix2t64{a} libproc2-0{a} libpsl5t64{a} libpsm2-2{a} librdmacm1t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libstdc++-14-dev{a} libtasn1-6{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} libxml2-16{a} libxml2-dev{a} libxnvctrl0{a} libz3-4{a} libze1{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libfl-dev libldap-common libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget xauth 0 packages upgraded, 146 newly installed, 0 to remove and 0 not upgraded. Need to get 212 MB of archives. After unpacking 1021 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libfido2-1 amd64 1.16.0-2 [78.8 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 23 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 openssh-client amd64 1:10.0p1-8 [986 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.9-2 [443 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libcurl4t64 amd64 8.16.0-4 [408 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 56 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 62 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 gengetopt amd64 2.23+dfsg1-1 [173 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libgfortran-15-dev amd64 15.2.0-4 [886 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-4 [78.8 MB] Get: 73 http://deb.debian.org/debian forky/main amd64 gfortran-15 amd64 15.2.0-4 [17.9 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4 [1276 B] Get: 75 http://deb.debian.org/debian forky/main amd64 gfortran amd64 4:15.2.0-4 [1436 B] Get: 76 http://deb.debian.org/debian forky/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libibverbs1 amd64 56.1-1+b1 [63.0 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 ibverbs-providers amd64 56.1-1+b1 [361 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 82 http://deb.debian.org/debian forky/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 83 http://deb.debian.org/debian forky/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 84 http://deb.debian.org/debian forky/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libamdhip64-5 amd64 5.7.1-7 [8938 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 libgcc-14-dev amd64 14.3.0-8 [2670 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libstdc++-14-dev amd64 14.3.0-8 [2673 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-5 [10.6 MB] Get: 95 http://deb.debian.org/debian forky/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 96 http://deb.debian.org/debian forky/main amd64 libboost-serialization1.83.0 amd64 1.83.0-5 [343 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 libboost-serialization1.83-dev amd64 1.83.0-5 [383 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 librdmacm1t64 amd64 56.1-1+b1 [71.0 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libpmix2t64 amd64 6.0.0+really5.0.8-1 [668 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libibumad3 amd64 56.1-1+b1 [30.1 kB] Get: 118 http://deb.debian.org/debian forky/main amd64 libibmad5 amd64 56.1-1+b1 [44.9 kB] Get: 119 http://deb.debian.org/debian forky/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 120 http://deb.debian.org/debian forky/main amd64 libopenmpi40 amd64 5.0.8-10+b1 [2414 kB] Get: 121 http://deb.debian.org/debian forky/main amd64 libboost-mpi1.83.0 amd64 1.83.0-5 [276 kB] Get: 122 http://deb.debian.org/debian forky/main amd64 openmpi-common all 5.0.8-10 [97.5 kB] Get: 123 http://deb.debian.org/debian forky/main amd64 libnl-3-dev amd64 3.11.0-2 [110 kB] Get: 124 http://deb.debian.org/debian forky/main amd64 libnl-route-3-dev amd64 3.11.0-2 [235 kB] Get: 125 http://deb.debian.org/debian forky/main amd64 libibverbs-dev amd64 56.1-1+b1 [659 kB] Get: 126 http://deb.debian.org/debian forky/main amd64 libnuma-dev amd64 2.0.19-1 [36.5 kB] Get: 127 http://deb.debian.org/debian forky/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get: 128 http://deb.debian.org/debian forky/main amd64 libltdl-dev amd64 2.5.4-5 [168 kB] Get: 129 http://deb.debian.org/debian forky/main amd64 libhwloc-dev amd64 2.12.2-1 [257 kB] Get: 130 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 131 http://deb.debian.org/debian forky/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 132 http://deb.debian.org/debian forky/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 133 http://deb.debian.org/debian forky/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 134 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 135 http://deb.debian.org/debian forky/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 136 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 137 http://deb.debian.org/debian forky/main amd64 openmpi-bin amd64 5.0.8-10+b1 [190 kB] Get: 138 http://deb.debian.org/debian forky/main amd64 libopenmpi-dev amd64 5.0.8-10+b1 [1090 kB] Get: 139 http://deb.debian.org/debian forky/main amd64 mpi-default-dev amd64 1.19 [3432 B] Get: 140 http://deb.debian.org/debian forky/main amd64 libboost-mpi1.83-dev amd64 1.83.0-5 [296 kB] Get: 141 http://deb.debian.org/debian forky/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 142 http://deb.debian.org/debian forky/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 143 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 144 http://deb.debian.org/debian forky/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 145 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-2 [349 kB] Get: 146 http://deb.debian.org/debian forky/main amd64 libxml2-dev amd64 2.14.6+dfsg-0.1 [756 kB] Fetched 212 MB in 5s (39.1 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 ... 19898 files and directories currently installed.) Preparing to unpack .../000-m4_1.4.20-2_amd64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package flex. Preparing to unpack .../001-flex_2.6.4-8.2+b4_amd64.deb ... Unpacking flex (2.6.4-8.2+b4) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../002-libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../003-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../007-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.41.2-1_amd64.deb ... Unpacking bsdextrautils (2.41.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../013-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../015-libedit2_3.1-20250104-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20250104-1) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../016-libcbor0.10_0.10.2-2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../017-libfido2-1_1.16.0-2_amd64.deb ... Unpacking libfido2-1:amd64 (1.16.0-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../018-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../019-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../020-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../021-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../022-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../023-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package openssh-client. Preparing to unpack .../024-openssh-client_1%3a10.0p1-8_amd64.deb ... Unpacking openssh-client (1:10.0p1-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../025-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../026-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../027-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../028-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package bison. Preparing to unpack .../029-bison_2%3a3.8.2+dfsg-1+b2_amd64.deb ... Unpacking bison (2:3.8.2+dfsg-1+b2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../030-cmake-data_4.1.1+really3.31.6-2_all.deb ... Unpacking cmake-data (4.1.1+really3.31.6-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../031-libxml2-16_2.14.6+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../032-libarchive13t64_3.7.4-4+b1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../033-libnghttp3-9_1.12.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.12.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../034-libngtcp2-16_1.16.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.16.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../035-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../036-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../037-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../038-libsasl2-modules-db_2.1.28+dfsg1-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../039-libsasl2-2_2.1.28+dfsg1-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../040-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../041-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libngtcp2-crypto-ossl0:amd64. Preparing to unpack .../042-libngtcp2-crypto-ossl0_1.16.0-1_amd64.deb ... Unpacking libngtcp2-crypto-ossl0:amd64 (1.16.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../043-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../044-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../045-libp11-kit0_0.25.9-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.9-2) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../046-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../047-libgnutls30t64_3.8.10-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../048-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../049-libssh2-1t64_1.11.1-1_amd64.deb ... 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Setting up libblas-dev:amd64 (3.12.1-7) ... 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 automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up flex (2.6.4-8.2+b4) ... Setting up liblapack3:amd64 (3.12.1-7) ... 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 libboost1.83-dev:amd64 (1.83.0-5) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... 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 (1.83.0-5) ... 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Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libdrm2:amd64 (2.4.125-2) ... Setting up libnl-3-dev:amd64 (3.11.0-2) ... Setting up groff-base (1.23.0-9) ... Setting up libhwloc-dev:amd64 (2.12.2-1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.125-2) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up gfortran-15-x86-64-linux-gnu (15.2.0-4) ... Setting up libibverbs1:amd64 (56.1-1+b1) ... Setting up ibverbs-providers:amd64 (56.1-1+b1) ... Setting up openssh-client (1:10.0p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libhwloc-plugins:amd64 (2.12.2-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4) ... Setting up libnl-route-3-dev:amd64 (3.11.0-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (6.0.0+really5.0.8-1) ... Setting up librdmacm1t64:amd64 (56.1-1+b1) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up gfortran-15 (15.2.0-4) ... Setting up libfabric1:amd64 (2.1.0-1.1) ... Setting up libcurl4t64:amd64 (8.16.0-4) ... Setting up debhelper (13.28) ... Setting up libibverbs-dev:amd64 (56.1-1+b1) ... Setting up gfortran (4:15.2.0-4) ... 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 libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up cmake (4.1.1+really3.31.6-2) ... Setting up libamdhip64-5:amd64 (5.7.1-7) ... Setting up libucx0:amd64 (1.19.0+ds-1) ... Setting up libopenmpi40:amd64 (5.0.8-10+b1) ... Setting up libboost-mpi1.83.0 (1.83.0-5) ... Setting up openmpi-bin (5.0.8-10+b1) ... 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 Setting up libopenmpi-dev:amd64 (5.0.8-10+b1) ... 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 (1.19) ... Setting up libboost-mpi1.83-dev (1.83.0-5) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Processing triggers for libc-bin (2.41-12) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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_1.0.11-14_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-14 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 .. -- The CXX compiler identification is GNU 15.2.0 -- 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 15.2.0 -- 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 15.2.0 -- 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 "2.14.6") mpilib is /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi included path is -- Configuring done (9.1s) 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 (0.1s) 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 -j40 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 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 [ 1%] [BISON][MyParser2] Building parser with bison 3.8.2 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/gb.tab.c.o [ 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/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 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/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/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 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_new_sequence': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:35:1: warning: old-style function definition [-Wold-style-definition] 35 | seq_new_sequence(locus, type, definition, length) | ^~~~~~~~~~~~~~~~ /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; | ^~~~ /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:288:1: warning: old-style function definition [-Wold-style-definition] 288 | seq_add_comment(e, s) | ^~~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_set_definition': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:327:1: warning: old-style function definition [-Wold-style-definition] 327 | seq_set_definition(e, s) | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_set_accession': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:352:1: warning: old-style function definition [-Wold-style-definition] 352 | seq_set_accession(e, s) | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_free_comments': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:369:1: warning: old-style function definition [-Wold-style-definition] 369 | seq_free_comments(c) | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_free': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:383:1: warning: old-style function definition [-Wold-style-definition] 383 | seq_free(entries) | ^~~~~~~~ gb.y: In function 'add_to_seq': gb.y:399:1: warning: old-style function definition [-Wold-style-definition] 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 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 [ 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/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' [ 5%] 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/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 [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o [ 8%] 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 [ 10%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o [ 20%] 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/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 [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o [ 28%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o [ 28%] 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/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 [ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.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/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/Tokenizer.cc.o -MF CMakeFiles/prime-phylo.dir/Tokenizer.cc.o.d -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c 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-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 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 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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 -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 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 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/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 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 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 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-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 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 /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); | ^ /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 /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 ) | ^~~~~~~ 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 *' [ 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 [ 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/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 [ 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/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 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 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; | ^~ 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 '< >' [ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o [ 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/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 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 [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.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/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 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 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 [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o [ 36%] 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/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 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 [ 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/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 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 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 [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o [ 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/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 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 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 [ 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 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 '< >' [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o [ 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/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 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 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$. | ^~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' 54 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\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/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$. | ^~ 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; | ^~~~~~~~~~~~~~~~ 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 '< >' 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; | ^~~~~~~~~~~~~~~~ /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. | ~~~~~~~~~^~~~~~~ /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; | ^~~~ 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/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 /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; | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /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/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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /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/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(), | ^~~~~~~~ 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; | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /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; | ^~~~~~~~ /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/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/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); | ^~~~ 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. | ^~~ [ 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 /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++) | ~~^~~~~~~~~~ [ 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 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; | ^~~~~~~~ [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.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 [ 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/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 [ 44%] 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 [ 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 [ 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 /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 [ 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/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 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 [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o [ 49%] 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/EdgeDiscBDMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o.d -o 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-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 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 [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o [ 50%] 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/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 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/EdgeDiscGSR.cc.o [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o [ 53%] 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 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 [ 54%] 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/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/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 [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o cd 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-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 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 [ 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 [ 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 [ 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 [ 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 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; | ^~ [ 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 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; | ^~ 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/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 '< >' 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 '< >' /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] [ 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/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; | ^~~~~~~~~~~~~~~~ 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; | ^~ /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/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; | ^~~~~~~~~~~~~~~~ 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 '< >' /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; | ^~~~~~~ [ 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 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 | ^~~~~~~~~~~~~~~~~~~~~~~ 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 '< >' [ 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/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 '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:60:18: warning: 'virtual void beep::ReconciliationModel::setGamma(const beep::GammaMap&)' was hidden [-Woverloaded-virtual=] 60 | virtual void setGamma(const GammaMap& newGamma); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:188:10: note: by 'void beep::EnumerateLabeledReconciliationModel::setGamma(unsigned int)' 188 | void setGamma(unsigned unique); | ^~~~~~~~ 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/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++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/bits/specfun.h:43, from /usr/include/c++/15/cmath:3913, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 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 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 '< >' 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; | ^~~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o 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++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/vector:64, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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/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/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, | ^~~~~~~~~~~~~~~~~~~~~~ /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/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 | ^~~~~~~~~~~~~~~~~~~~~~~ /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(); | ^~~~~~ 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/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); | ^~~~~~~~ /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; | ^~~~~~~~~~~~~~~~~ [ 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 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/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: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/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:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 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 [ 68%] 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/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$. | ^~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o [ 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/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 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 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 '< >' [ 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/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 '< >' [ 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 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/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 '< >' 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; | ^~~~~~~~ /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/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 '< >' [ 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 /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; | ^~~~~~~ [ 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 [ 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 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); | ^~~~~~~~ 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:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/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: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/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: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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 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/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:11: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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 '< >' /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; | ^~~~~~~ [ 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 [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o [ 75%] 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/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 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 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 '< >' [ 76%] 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 [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o [ 77%] 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/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 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 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); | ^~~~~~~~ /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: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: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/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o [ 78%] 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/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 [ 78%] 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/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 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 /usr/include/c++/15/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++/15/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 \ | ^~~~~~~ [ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o [ 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/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 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 /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/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/BirthDeathProbs.hh:58:19: warning: 'virtual beep::Tree& beep::BirthDeathProbs::getStree() const' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& getStree() const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:40:17: note: by 'beep::HybridTree& beep::BirthDeathInHybridProbs::getStree()' 40 | HybridTree& getStree(); | ^~~~~~~~ /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=] 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); | ^~~~~~~~ /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); | ^~~~~~~~ /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: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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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); | ^~~~~~~~ /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: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: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/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 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 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); | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:58:19: warning: 'virtual beep::Tree& beep::BirthDeathProbs::getStree() const' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& getStree() const; | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:40:17: note: by 'beep::HybridTree& beep::BirthDeathInHybridProbs::getStree()' 40 | HybridTree& getStree(); | ^~~~~~~~ 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); | ^~~~~~~~ /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: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: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/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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); | ^~~~~~~~ /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: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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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); | ^~~~~~~~ /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: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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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 '< >' 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); | ^~~~~~~~ /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: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: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/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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); | ^~~~~~~~ /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: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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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: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/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: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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /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() | ^~~~~~~~~ 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); | ^~~~~~~~ /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/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector*, beep::StrStrMap*, std::map*, std::map*)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:29: warning: 'idInt' may be used uninitialized [-Wmaybe-uninitialized] 1049 | new_node = S.addNode(l, r, idInt, name); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:959:9: note: 'idInt' was declared here 959 | int idInt; | ^~~~~ 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); | ^~~~~~~~ /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: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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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 '< >' 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$. | ^~ /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/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 /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 '< >' 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 '< >' 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); | ^~~~~~~~ /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/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/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/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/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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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); | ^~~~~~~~ /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: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: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/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ 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/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 '< >' /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/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. | ^~~ 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); | ^~~~ 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/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++) { | ~~^~~~~~~~~~~~~~ [ 81%] Linking CXX shared library libprime-phylo.so cd 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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' [ 82%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h [ 85%] Generating cmdline.c, cmdline.h [ 84%] 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' make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 84%] Generating cmdline.c, cmdline.h make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build 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 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 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/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 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/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 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/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 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 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 [ 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 && /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/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=" 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/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/tree2leafnames /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/tree2leafnames /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.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 /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/chainsaw /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.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/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build make[3]: Entering 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[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 src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build make[3]: Entering directory '/build/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 -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]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build cd /build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /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/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 -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/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 make[3]: Leaving 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 -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 86%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o 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 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize -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/treesize/CMakeFiles/treesize.dir/treesize.cc.o -MF CMakeFiles/treesize.dir/treesize.cc.o.d -o CMakeFiles/treesize.dir/treesize.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc [ 86%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o [ 87%] 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/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 [ 88%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.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 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-c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc [ 94%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o cd /build/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 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); | ^~~~~~~~ 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/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/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:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /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/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: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: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: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/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /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) | ^ 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: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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /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) { | ^ [ 94%] Linking CXX executable tree2leafnames [ 95%] Linking CXX executable treesize 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 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 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 /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 tree2leafnames 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 '< >' /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 [ 96%] Built target treesize /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) { | ^ 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++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/algorithm:62, 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | 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++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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/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/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/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/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/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/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 '< >' 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. | ^~~ /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/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/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; | ^~~~~~~~ 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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /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/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/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: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/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:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /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) { | ^ [ 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 [ 97%] 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 /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 /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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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' [ 99%] Built target primeDLRS [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 -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 /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /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 -j40 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' in '../prime-phylo_1.0.11-14_amd64.deb'. dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-14_amd64.deb'. dpkg-genbuildinfo --build=binary -O../prime-phylo_1.0.11-14_amd64.buildinfo dpkg-genchanges --build=binary -O../prime-phylo_1.0.11-14_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/3674162 and its subdirectories I: Current time: Sun Oct 19 10:08:54 -12 2025 I: pbuilder-time-stamp: 1760911734 Sun Oct 19 22:08:56 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sun Oct 19 22:08:56 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sun Oct 19 22:11:07 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sun Oct 19 22:11:08 UTC 2025 I: prime-phylo_1.0.11-14_amd64.changes: Format: 1.8 Date: Mon, 22 Sep 2025 21:44:48 +0200 Source: prime-phylo Binary: prime-phylo prime-phylo-dbgsym Architecture: amd64 Version: 1.0.11-14 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: 1097647 1113421 Changes: prime-phylo (1.0.11-14) unstable; urgency=medium . * gcc-15.patch: new: fix build failures with gcc-15. (Closes: #1097647) * cmake-4.patch: new: fix build failure past cmake 4. (Closes: #1113421) * d/watch: convert to v5 untrackable upstream. * d/control: R³ now defaults to no, thus redundant. * d/patches/*: normalize Last-Update timestamp. * d/control: declare compliance to standards version 4.7.2. Checksums-Sha1: a56a48bfd750d72c355b334dd59f28c19f2bb7e6 10033208 prime-phylo-dbgsym_1.0.11-14_amd64.deb 2f8c1e11ca211a8e9953589e60b10a0f3412b609 8875 prime-phylo_1.0.11-14_amd64.buildinfo ab37223818b35b17d4ea265773e02870a10b8290 834460 prime-phylo_1.0.11-14_amd64.deb Checksums-Sha256: 500aa8882a6f47ad0fb389fd87bf86bda28409081cfc1fd6d07410576473bd40 10033208 prime-phylo-dbgsym_1.0.11-14_amd64.deb a717b78142a2aa4925faea4ef4533a3a9dde613dcce77837c1346fcd649d0926 8875 prime-phylo_1.0.11-14_amd64.buildinfo eed0ccc2a5583be9c427e725898ae14f2e3140abfe5254f2182e97da17730090 834460 prime-phylo_1.0.11-14_amd64.deb Files: 768185006a6ea0aba77d76357978677f 10033208 debug optional prime-phylo-dbgsym_1.0.11-14_amd64.deb 106920d396efacb889515e42d04de42f 8875 science optional prime-phylo_1.0.11-14_amd64.buildinfo 182edef4474abc9bbeb2269e179705e3 834460 science optional prime-phylo_1.0.11-14_amd64.deb Sun Oct 19 22:11:08 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_23-75726.service; invocation ID: fe7d9b86dfa048f3911b11b97fe2ea44 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.qsySVxRZ/prime-phylo_1.0.11-14.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.qsySVxRZ/prime-phylo_1.0.11-14.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.qsySVxRZ/prime-phylo_1.0.11-14.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.qsySVxRZ/b1/prime-phylo_1.0.11-14_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.qsySVxRZ/b2/prime-phylo_1.0.11-14_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 204ms CPU time consumed: 172ms Memory peak: 17.8M (swap: 0B) Sun Oct 19 22:11:09 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 19 22:11:09 UTC 2025 I: prime-phylo from forky built successfully and reproducibly on amd64. Sun Oct 19 22:11:10 UTC 2025 I: Removing signed prime-phylo_1.0.11-14_amd64.buildinfo.asc files: removed './b1/prime-phylo_1.0.11-14_amd64.buildinfo.asc' removed './b2/prime-phylo_1.0.11-14_amd64.buildinfo.asc'