sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | prime-phylo 1.0.11-13 (amd64) Wed, 22 Jan 2025 09:31:47 +0000 | +==============================================================================+ Package: prime-phylo Version: 1.0.11-13 Source Version: 1.0.11-13 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Wed, 22 Jan 2025 09:31:47 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup prime-phylo_1.0.11-13 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup prime-phylo_1.0.11-13 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Wed, 22 Jan 2025 09:31:47 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:2 http://localhost:3142/debian sid InRelease [205 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:3 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [147 kB] Get:5 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Get:4 http://localhost:3142/debian sid/main Sources T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [147 kB] Get:6 http://deb.debian.org/debian unstable InRelease [205 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [144 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [144 kB] Fetched 829 kB in 6s (142 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2494 kB of archives. After this operation, 4096 B disk space will be freed. Get:1 http://deb.debian.org/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.24 [1114 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 apt amd64 2.9.24 [1380 kB] Fetched 2494 kB in 0s (112 MB/s) (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 ... 23043 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.24_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.24) over (2.9.23) ... Setting up libapt-pkg6.0t64:amd64 (2.9.24) ... (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 ... 23043 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.24_amd64.deb ... Unpacking apt (2.9.24) over (2.9.23) ... Setting up apt (2.9.24) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Fetch source files Wed, 22 Jan 2025 09:31:56 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/prime-phylo_1.0.11-13.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 22 Jan 2025 09:31:57 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged 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, build-essential Filtered 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, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/prime-phylo-q2I051/resolver-06LKZv/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/prime-phylo-q2I051/resolver-06LKZv/apt_archive ./ InRelease Get:2 copy:/build/prime-phylo-q2I051/resolver-06LKZv/apt_archive ./ Release [609 B] Ign:3 copy:/build/prime-phylo-q2I051/resolver-06LKZv/apt_archive ./ Release.gpg Get:4 copy:/build/prime-phylo-q2I051/resolver-06LKZv/apt_archive ./ Sources [770 B] Get:5 copy:/build/prime-phylo-q2I051/resolver-06LKZv/apt_archive ./ Packages [809 B] Fetched 2188 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bison bsdextrautils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docutils-common dwz file flex gengetopt gettext gettext-base gfortran gfortran-14 gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libcbor0.10 libcom-err2 libcurl4t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 librhash1 librtmp1 libssh2-1t64 libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-dev libxnvctrl0 libz3-4 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl po-debconf procps python-babel-localedata python3 python3-alabaster python3-autocommand python3-babel python3-certifi python3-chardet python3-charset-normalizer python3-defusedxml python3-docutils python3-idna python3-imagesize python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pygments python3-requests python3-roman python3-snowballstemmer python3-sphinx python3-typeguard python3-typing-extensions python3-urllib3 python3.13 python3.13-minimal sensible-utils sgml-base sphinx-common tzdata xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flex-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-14-multilib gfortran-14-doc libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost-graph1.83-dev libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk pkg-config m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk python3-venv python-charset-normalizer-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-jinja2-doc python3-setuptools python-pygments-doc ttf-bitstream-vera python3-cryptography python3-openssl python3-socks python-requests-doc python3-stemmer dvipng dvisvgm fonts-freefont-otf imagemagick latexmk libjs-mathjax python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-extra texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.13-venv python3.13-doc binfmt-support sgml-base-doc Recommended packages: libfl-dev curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl krb5-locales libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl psmisc linux-sysctl-defaults libpaper-utils python3-pil The following NEW packages will be installed: autoconf automake autopoint autotools-dev bison bsdextrautils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docutils-common dwz file flex gengetopt gettext gettext-base gfortran gfortran-14 gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libcbor0.10 libcom-err2 libcurl4t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 librhash1 librtmp1 libssh2-1t64 libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-dev libxnvctrl0 libz3-4 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl po-debconf procps python-babel-localedata python3 python3-alabaster python3-autocommand python3-babel python3-certifi python3-chardet python3-charset-normalizer python3-defusedxml python3-docutils python3-idna python3-imagesize python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pygments python3-requests python3-roman python3-snowballstemmer python3-sphinx python3-typeguard python3-typing-extensions python3-urllib3 python3.13 python3.13-minimal sbuild-build-depends-main-dummy sensible-utils sgml-base sphinx-common tzdata xml-core zlib1g-dev 0 upgraded, 181 newly installed, 0 to remove and 0 not upgraded. Need to get 175 MB of archives. After this operation, 841 MB of additional disk space will be used. Get:1 copy:/build/prime-phylo-q2I051/resolver-06LKZv/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [936 B] Get:2 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-1 [259 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:37 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.4-2 [2267 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.4-2 [12.0 MB] Get:59 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get:65 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 gengetopt amd64 2.23+dfsg1-1 [173 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-14 [837 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-14 [881 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-14 [11.7 MB] Get:77 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-14 [13.5 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get:79 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get:80 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 55.0-1 [62.2 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 55.0-1 [351 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-6 [210 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-20+b1 [23.6 MB] Get:87 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:88 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:89 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-4 [161 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get:98 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:99 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4 [333 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4 [373 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 55.0-1 [70.2 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.6-1 [652 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 55.0-1 [28.5 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 55.0-1 [43.3 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.6-3 [2360 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83.0 amd64 1.83.0-4 [271 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.6-3 [97.0 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 55.0-1 [648 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-2 [415 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-2 [165 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-4 [616 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:152 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get:158 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-2 [120 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get:163 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:165 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:167 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:168 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get:169 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-4 [468 kB] Get:170 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.6-1 [3962 kB] Get:171 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:172 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.6-3 [188 kB] Get:173 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get:174 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get:175 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83-dev amd64 1.83.0-4 [290 kB] Get:176 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get:177 http://deb.debian.org/debian unstable/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get:178 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-6 [10.4 MB] Get:179 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:180 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB] Get:181 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Preconfiguring packages ... Fetched 175 MB in 1s (167 MB/s) Selecting previously unselected package m4. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b4_amd64.deb ... Unpacking flex (2.6.4-8.2+b4) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.1-3_amd64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:amd64 (3.13.1-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... 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Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libboost1.83-dev:amd64 (1.83.0-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up gengetopt (2.23+dfsg1-1) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcbor0.10:amd64 (0.10.2-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libibumad3:amd64 (55.0-1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libibmad5:amd64 (55.0-1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 22 09:32:17 UTC 2025. Universal Time is now: Wed Jan 22 09:32:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-serialization1.83.0:amd64 (1.83.0-4) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up autopoint (0.23.1-1) ... Setting up icu-devtools (72.1-6) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libltdl7:amd64 (2.5.4-2) ... Setting up libgfortran5:amd64 (14.2.0-14) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up bison (2:3.8.2+dfsg-1+b2) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.6-3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.4-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.15.0-1+b1) ... Setting up openssl (3.4.0-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3) ... Setting up libicu-dev:amd64 (72.1-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libblas-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-14) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up flex (2.6.4-8.2+b4) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up python3.13 (3.13.1-3) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-4) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up python3 (3.13.1-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-14) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.5.4-2) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-20+b1) ... Setting up python3-certifi (2024.12.14+ds-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up liblapack-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libboost-serialization-dev:amd64 (1.83.0.2+b2) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libhwloc-dev:amd64 (2.11.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up gfortran-14 (14.2.0-14) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libibverbs1:amd64 (55.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:amd64 (8.11.1-1+b1) ... Setting up ibverbs-providers:amd64 (55.0-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Setting up gfortran (4:14.2.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up sphinx-common (8.1.3-4) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (5.0.6-1) ... Setting up cmake (3.31.4-2) ... Setting up librdmacm1t64:amd64 (55.0-1) ... Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up debhelper (13.24.1) ... Setting up libibverbs-dev:amd64 (55.0-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi40:amd64 (5.0.6-3) ... Setting up libboost-mpi1.83.0 (1.83.0-4) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Processing triggers for libc-bin (2.40-5) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-4) ... Setting up libpmix-dev:amd64 (5.0.6-1) ... Setting up libopenmpi-dev:amd64 (5.0.6-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Setting up libboost-mpi1.83-dev (1.83.0-4) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures Wed, 22 Jan 2025 09:32:26 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Wed, 22 Jan 2025 09:32:26 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 apt_2.9.24 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 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perl-modules-5.40_5.40.1-1 pinentry-curses_1.3.1-2 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 python-babel-localedata_2.16.0-1 python3_3.13.1-2 python3-alabaster_0.7.16-0.1 python3-autocommand_2.2.2-3 python3-babel_2.16.0-1 python3-certifi_2024.12.14+ds-1 python3-chardet_5.2.0+dfsg-2 python3-charset-normalizer_3.4.0-1+b1 python3-defusedxml_0.7.1-3 python3-docutils_0.21.2+dfsg-2 python3-idna_3.8-2 python3-imagesize_1.4.1-1 python3-inflect_7.3.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-jinja2_3.1.3-2 python3-markupsafe_2.1.5-1+b2 python3-minimal_3.13.1-2 python3-more-itertools_10.6.0-1 python3-packaging_24.2-1 python3-pkg-resources_75.6.0-1 python3-pygments_2.18.0+dfsg-2 python3-requests_2.32.3+dfsg-1 python3-roman_4.2-1 python3-snowballstemmer_2.2.0-4 python3-sphinx_8.1.3-4 python3-typeguard_4.4.1-1 python3-typing-extensions_4.12.2-2 python3-urllib3_2.3.0-1 python3.13_3.13.1-3 python3.13-minimal_3.13.1-3 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sphinx-common_8.1.3-4 sqv_1.2.1-5 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 tzdata_2025a-1 usr-is-merged_39+nmu2 util-linux_2.40.4-1 xml-core_0.19 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Wed, 22 Jan 2025 09:32:26 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prime-phylo Binary: prime-phylo Architecture: any Version: 1.0.11-13 Maintainer: Debian Med Packaging Team Uploaders: Erik Sjolund , Andreas Tille , Étienne Mollier Homepage: http://prime.sbc.su.se Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev Package-List: prime-phylo deb science optional arch=any Checksums-Sha1: 1dd3b086599e29f6a17319f8ebe294cd6eed0c07 750651 prime-phylo_1.0.11.orig.tar.gz 1b610ab09a7f030983645b55c899925f1274795b 11008 prime-phylo_1.0.11-13.debian.tar.xz Checksums-Sha256: 5d46b4e528417bb4a0be56756069f255f86ab58b28b55fa6a96983f10585bd8d 750651 prime-phylo_1.0.11.orig.tar.gz c038988e04bff12b839bb04944b83adf4f3c6fd919e3eedde830f6d8cbfdbd58 11008 prime-phylo_1.0.11-13.debian.tar.xz Files: 0356071434de01edf92a1b9182ed6ef1 750651 prime-phylo_1.0.11.orig.tar.gz 5dd29777cf77e181037010c776918890 11008 prime-phylo_1.0.11-13.debian.tar.xz Dgit: 145774abd804a6a885854671c901ccad9cc48798 debian archive/debian/1.0.11-13 https://git.dgit.debian.org/prime-phylo -----BEGIN PGP SIGNATURE----- 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signature: No public key dpkg-source: warning: cannot verify inline signature for ./prime-phylo_1.0.11-13.dsc: no acceptable signature found dpkg-source: info: extracting prime-phylo in /build/prime-phylo-q2I051/prime-phylo-1.0.11 dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-Boost160.patch dpkg-source: info: applying fix-gcc-8.patch dpkg-source: info: applying 0003-Fix-build-with-Boost-1.67.patch dpkg-source: info: applying 0004-fix-gcc10-build.patch dpkg-source: info: applying fix-ftbfs-with-gcc13.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying openmpi5.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Wed, 22 Jan 2025 09:32:27 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network prime-phylo_1.0.11-13 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network prime-phylo_1.0.11-13 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/prime-phylo-q2I051/prime-phylo-1.0.11 SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-afe0f98b-e5a3-400e-bf47-b9d82c7ef0c7 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --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 dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building prime-phylo using existing ./prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building prime-phylo in prime-phylo_1.0.11-13.debian.tar.xz dpkg-source: info: building prime-phylo in prime-phylo_1.0.11-13.dsc debian/rules binary dh binary --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11' dh_auto_configure -- \ -Dofficial_binary_packaging=on \ -Dprime_dynamic=on \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \ -DCMAKE_BUILD_TYPE=RELEASE cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- The Fortran compiler identification is GNU 14.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- The C compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so hittade /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for Fortran cheev -- Looking for Fortran cheev - not found -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found BISON: /usr/bin/bison (found version "3.8.2") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") CMake Warning (dev) at src/cxx/CMakeLists.txt:92 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.40.0") found components: mpi serialization -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14") mpilib is /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi included path is CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDTLSR". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDTLSR/CMakeLists.txt:30 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDLRS". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDLRS/CMakeLists.txt:27 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "showtree". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/tools/showtree/CMakeLists.txt:12 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:120 (if): Policy CMP0053 is not set: Simplify variable reference and escape sequence evaluation. Run "cmake --help-policy CMP0053" for policy details. Use the cmake_policy command to set the policy and suppress this warning. For input: '@CMAKE_SOURCE_DIR@/excluded_from_release' the old evaluation rules produce: '/build/prime-phylo-q2I051/prime-phylo-1.0.11/excluded_from_release' but the new evaluation rules produce: '@CMAKE_SOURCE_DIR@/excluded_from_release' Using the old result for compatibility since the policy is not set. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (3.8s) CMake Warning (dev) at src/cxx/tools/tree2leafnames/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11' dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-q2I051/prime-phylo-1.0.11 -B/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 [ 1%] [BISON][MyParser2] Building parser with bison 3.8.2 cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/flex -o/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:265:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] 265 | printf("%9d", char_counter + 1); | ^~~~~ ~~~~~~~~~~~~~~~~ | | | long int /build/prime-phylo-q2I051/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; | ^~~~ [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_add_comment’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:303:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 303 | tmp->text = strdup(s); | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by ‘malloc’ 301 | tmp = (struct comment *) malloc(sizeof(struct comment *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:304:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 304 | tmp->next = NULL; | ^~ /build/prime-phylo-q2I051/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 *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqreader.l: In function ‘seq_read’: seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable] /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level: /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function] 1864 | static int input (void) | ^~~~~ /build/prime-phylo-q2I051/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 ) | ^~~~~~~ [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y: In function ‘add_to_seq’: gb.y:403:9: warning: unused variable ‘new_buf’ [-Wunused-variable] [ 4%] Linking C shared library libprime-phylo-sfile.so cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function ‘NHX_debug_print’: /build/prime-phylo-q2I051/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 [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16: warning: ‘input’ defined but not used [-Wunused-function] 1597 | static int input (void) | ^~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17: warning: ‘yyunput’ defined but not used [-Wunused-function] 1554 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function ‘new_annotation’: /build/prime-phylo-q2I051/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); | ^ [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -MF CMakeFiles/prime-phylo.dir/NHXparse.c.o.d -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c 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 *’ [ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -MF CMakeFiles/prime-phylo.dir/AnError.cc.o.d -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o -MF CMakeFiles/prime-phylo.dir/Beep.cc.o.d -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o -MF CMakeFiles/prime-phylo.dir/Hacks.cc.o.d -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Hacks.cc [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc:4: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-q2I051/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; | ^~ [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o -MF CMakeFiles/prime-phylo.dir/PRNG.cc.o.d -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -MF CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o.d -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -MF CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function ‘void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 405 | catch(std::exception e) | ^ /build/prime-phylo-q2I051/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) | ^ [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -MF CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -MF CMakeFiles/prime-phylo.dir/Probability.cc.o.d -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -MF CMakeFiles/prime-phylo.dir/Tokenizer.cc.o.d -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -MF CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o.d -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TimeEstimator.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.cc [ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/DiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscTree.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscTree.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscTree.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.hh:1, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:3: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: /build/prime-phylo-q2I051/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; | ^~~~~~~~~~~~~~~~ [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o -MF CMakeFiles/prime-phylo.dir/EpochTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: /build/prime-phylo-q2I051/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; | ^~~~~~~~~~~~~~~~ [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -MF CMakeFiles/prime-phylo.dir/InvMRCA.cc.o.d -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/InvMRCA.cc [ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o -MF CMakeFiles/prime-phylo.dir/Node.cc.o.d -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Node.cc [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.cc [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/RandomTreeGenerator.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc:3: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -MF CMakeFiles/prime-phylo.dir/StrStrMap.cc.o.d -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/StrStrMap.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o -MF CMakeFiles/prime-phylo.dir/Tree.cc.o.d -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc:3: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizer.cc [ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizers.cc [ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc: In constructor ‘beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const beep::Real&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:26:15: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null] 26 | old_times(NULL), | ^~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:6: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:27:15: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null] 27 | old_rates(NULL), | ^~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:28:17: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null] 28 | old_lengths(NULL), | ^~~~ /build/prime-phylo-q2I051/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. | ~~~~~~~~~^~~~~~~ [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function ‘void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)’: /build/prime-phylo-q2I051/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; | ^~~~ [ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -MF CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o.d -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:6: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:7: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:8: /build/prime-phylo-q2I051/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; | ^~~~~~~~ [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC.cc [ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function ‘void beep::EdgeRateMCMC_common::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable ‘fparam’ [-Wunused-variable] 104 | Real fparam = std::log(rate) - 0.5 * variance * (rtime - 3.0 * ltime); | ^~~~~~ /build/prime-phylo-q2I051/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); | ^~~~~~ [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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); | ^~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function ‘void beep::EdgeWeightMCMC::showCurrentTree()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 106 | for (int i = 0; i < t.size(); i++) | ~~^~~~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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; | ^~~~~~~~ [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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; | ^~~~~~~~ [ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/prime-phylo-q2I051/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$. | ^~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -MF CMakeFiles/prime-phylo.dir/UniformDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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; | ^~~~~~~~ [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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; | ^~~~~~~~ [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/prime-phylo-q2I051/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. | ^~~ [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCModel.cc [ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCObject.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:6: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:7: /build/prime-phylo-q2I051/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; | ^~~~~~~~ [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc: In member function ‘virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable ‘check_number_nonupdate’ set but not used [-Wunused-but-set-variable] 78 | unsigned check_number_nonupdate = 0; | ^~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.cc [ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/MCMCSampler.cc [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/GSRSampler.cc [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleObserver.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.hh:14, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc:6: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.hh:19, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:6: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function ‘virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)’: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:337:27: warning: operation on ‘i’ may be undefined [-Wsequence-point] /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:337:27: warning: operation on ‘i’ may be undefined [-Wsequence-point] [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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, | ^~~~~~~~~~~~~~ [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc [ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/vector:62, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor ‘beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: ‘beep::EdgeDiscGSR::m_calculatedAtAndBelow’ will be initialized after [-Wreorder] 588 | bool m_calculatedAtAndBelow; | ^~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: ‘bool beep::EdgeDiscGSR::m_calculatedAtBars’ [-Wreorder] 583 | bool m_calculatedAtBars; | ^~~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, | ^~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function ‘void beep::EdgeDiscGSR::convertDensitiesToProbabilities()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 475 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable ‘xpt’ set but not used [-Wunused-but-set-variable] 485 | Point xpt = x.getPt(); | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 525 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable ‘parent’ [-Wunused-variable] 528 | Node *parent = u->getParent(); | ^~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function ‘beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)’: /build/prime-phylo-q2I051/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); | ^~~~~~~~ [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-q2I051/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; | ^~~~~~~ [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochBDTProbs::ABS_TOL’ of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-q2I051/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; | ^~~~~~~ [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc [ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc:5: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:9: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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, | ^~~~~~~~~~~~~~~~~~~~~~ [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.hh:8, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:2: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.hh:17: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘unsigned int beep::fastGEM::calcMaxProb(unsigned int)’: /build/prime-phylo-q2I051/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); | ^~~~~~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printSa()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1298:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1298 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLb()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1325:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1325 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLt()’: /build/prime-phylo-q2I051/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; | ^~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc [ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.hh:6, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc:5: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /build/prime-phylo-q2I051/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$. | ^~ [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:6: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function ‘void beep::ReconciliationSampler::setAttributesAndProbabilities()’: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.hh:16, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function ‘std::string beep::ReconciliationTimeModel::table4os() const’: /build/prime-phylo-q2I051/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; | ^~~~~~~ [ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.hh:12, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function ‘const std::string beep::ReconciliationTimeSampler::table4os() const’: /build/prime-phylo-q2I051/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; | ^~~~~~~ [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:6: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor ‘beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const std::string&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: ‘beep::ReconciliationTreeGenerator::R’ is initialized with itself [-Winit-self] 31 | ReconciliationTreeGenerator:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:20, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:22: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:11: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc [ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc:3: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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, | ^~~~~~~~~~ [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function ‘beep::Tree& beep::HybridTree::getBinaryTree() const’: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:5: /build/prime-phylo-q2I051/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); | ^~~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:5: /build/prime-phylo-q2I051/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); | ^~~~~~~~ [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeGenerator.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:6: /build/prime-phylo-q2I051/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); | ^~~~~~~~ [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:5: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: note: by ‘virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)’ 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:7: /build/prime-phylo-q2I051/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); | ^~~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: warning: ‘virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)’ was hidden [-Woverloaded-virtual=] /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:6: /build/prime-phylo-q2I051/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); | ^~~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:5: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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, | ^~~~~~~~~~ [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:5: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:8: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:6: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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); | ^~~~~~~~ [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:8: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:3: /build/prime-phylo-q2I051/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); | ^~~~~~~~ [ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:8: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:4: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /build/prime-phylo-q2I051/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. | ^~~ [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.cc [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc In file included from /usr/include/c++/14/ext/hash_map:60, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: /usr/include/c++/14/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:5: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc:2: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc:8: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SeqIO.cc [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:16: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: ‘std::ostream& beep::operator<<(std::ostream&, const SequenceType&)’ has not been declared within ‘beep’ 270 | ostream& beep::operator<<(ostream& os, const SequenceType& dt) | ^~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:8: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a ‘friend’ 56 | friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); | ^~~~~~~~ [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function ‘std::map beep::SequenceData::getBaseFrequencies()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 288 | for (int i = 0; i < seqType.alphabetSize(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:303:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 303 | for (int j = 0; j < seq.length(); j++) { | ~~^~~~~~~~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: /build/prime-phylo-q2I051/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. | ^~~ [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc [ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor ‘beep::LA_Matrix::LA_Matrix()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:19:5: warning: ‘beep::LA_Matrix::dim’ is initialized with itself [-Winit-self] 19 | LA_Matrix::LA_Matrix() | ^~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor ‘beep::LA_Matrix::LA_Matrix()’: /build/prime-phylo-q2I051/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), | ^~~ [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc [ 81%] Linking CXX shared library libprime-phylo.so cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/prime-phylo.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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"CMakeFiles/prime-phylo.dir/MatrixCache.cc.o" "CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o" "CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o" "CMakeFiles/prime-phylo.dir/SeqIO.cc.o" "CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o" "CMakeFiles/prime-phylo.dir/SequenceType.cc.o" "CMakeFiles/prime-phylo.dir/SequenceData.cc.o" "CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o" "CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o" "CMakeFiles/prime-phylo.dir/LA_Vector.cc.o" "CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o" "CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o" -L/usr/lib/x86_64-linux-gnu/liblapack.so -L/usr/lib/x86_64-linux-gnu/libblas.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu/liblapack.so:/usr/lib/x86_64-linux-gnu/libblas.so:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../sfile/libprime-phylo-sfile.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 81%] Built target prime-phylo make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 82%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM [ 82%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 82%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o -MF CMakeFiles/primeGEM.dir/troyo.cc.o.d -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:2: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:9: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C2’ of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C3’ of non-integral type [-fpermissive] 360 | static const Real C3 = 3.0 / 10.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C4’ of non-integral type [-fpermissive] 361 | static const Real C4 = 4.0 / 5.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C5’ of non-integral type [-fpermissive] 362 | static const Real C5 = 8.0 / 9.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A21’ of non-integral type [-fpermissive] 363 | static const Real A21 = 1.0 / 5.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A31’ of non-integral type [-fpermissive] 364 | static const Real A31 = 3.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A32’ of non-integral type [-fpermissive] 365 | static const Real A32 = 9.0 / 40.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A41’ of non-integral type [-fpermissive] 366 | static const Real A41 = 44.0 / 45.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A42’ of non-integral type [-fpermissive] 367 | static const Real A42 = -56.0 / 15.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A43’ of non-integral type [-fpermissive] 368 | static const Real A43 = 32.0 / 9.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A51’ of non-integral type [-fpermissive] 369 | static const Real A51 = 19372.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A52’ of non-integral type [-fpermissive] 370 | static const Real A52 = -25360.0 / 2187.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A53’ of non-integral type [-fpermissive] 371 | static const Real A53 = 64448.0 / 6561.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A54’ of non-integral type [-fpermissive] 372 | static const Real A54 = -212.0 / 729.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A61’ of non-integral type [-fpermissive] 373 | static const Real A61 = 9017.0 / 3168.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A62’ of non-integral type [-fpermissive] 374 | static const Real A62 = -355.0 / 33.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A63’ of non-integral type [-fpermissive] 375 | static const Real A63 = 46732.0 / 5247.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A64’ of non-integral type [-fpermissive] 376 | static const Real A64 = 49.0 / 176.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A65’ of non-integral type [-fpermissive] 377 | static const Real A65 = -5103.0 / 18656.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A71’ of non-integral type [-fpermissive] 378 | static const Real A71 = 35.0 / 384.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A73’ of non-integral type [-fpermissive] 379 | static const Real A73 = 500.0 / 1113.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A74’ of non-integral type [-fpermissive] 380 | static const Real A74 = 125.0 / 192.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A75’ of non-integral type [-fpermissive] 381 | static const Real A75 = -2187.0 / 6784.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A76’ of non-integral type [-fpermissive] 382 | static const Real A76 = 11.0 / 84.0; | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E1’ of non-integral type [-fpermissive] 383 | static const Real E1 = 71.0 / 57600.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E3’ of non-integral type [-fpermissive] 384 | static const Real E3 = -71.0 / 16695.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E4’ of non-integral type [-fpermissive] 385 | static const Real E4 = 71.0 / 1920.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E5’ of non-integral type [-fpermissive] 386 | static const Real E5 = -17253.0 / 339200.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E6’ of non-integral type [-fpermissive] 387 | static const Real E6 = 22.0 / 525.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E7’ of non-integral type [-fpermissive] 388 | static const Real E7 = -1.0 / 40.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D1’ of non-integral type [-fpermissive] 391 | static const Real D1 = -12715105075.0 / 11282082432.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D3’ of non-integral type [-fpermissive] 392 | static const Real D3 = 87487479700.0 / 32700410799.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D4’ of non-integral type [-fpermissive] 393 | static const Real D4 = -10690763975.0 / 1880347072.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D5’ of non-integral type [-fpermissive] 394 | static const Real D5 = 701980252875.0 / 199316789632.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D6’ of non-integral type [-fpermissive] 395 | static const Real D6 = -1453857185.0 / 822651844.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D7’ of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochBDTProbs::REL_TOL’ of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochBDTProbs::ABS_TOL’ of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:7: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:15: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:16: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:17: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:18: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function ‘int main(int, char**)’: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:27: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:28: /build/prime-phylo-q2I051/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; | ^~~~~~~~ [ 83%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -MF CMakeFiles/primeGEM.dir/cmdline.c.o.d -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c [ 83%] Linking CXX executable primeGEM cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/primeGEM.dir/link.d CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 83%] Built target primeGEM make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 83%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc [ 84%] Linking CXX executable primeDTLSR cd /build/prime-phylo-q2I051/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 In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:9: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/algorithm:60, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:1: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:10: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh: At global scope: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:14: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:15: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/primeDTLSR.dir/link.d CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 84%] Built target primeDTLSR make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /build/prime-phylo-q2I051/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. | ^~~ [ 85%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:27: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:28: /build/prime-phylo-q2I051/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; | ^~~~~~~~ cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 85%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:8: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc: In function ‘int main(int, char**)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:55:13: warning: enumeration value ‘input_format__NULL’ not handled in switch [-Wswitch] 55 | switch(args_info.input_format_arg) | ^ /build/prime-phylo-q2I051/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) { | ^ [ 86%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o -MF CMakeFiles/treesize.dir/cmdline.c.o.d -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.c [ 87%] Linking CXX executable treesize cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/treesize.dir/link.d CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 87%] Built target treesize make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 87%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 88%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:3: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:4: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function ‘void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:30:20: warning: variable ‘nw’ set but not used [-Wunused-but-set-variable] 30 | bool et, nt, bl, nw; | ^~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function ‘int main(int, char**)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:174:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 174 | if(args_info.tree_number_arg >= Tvec.size()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/prime-phylo-q2I051/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) | ^ [ 88%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c [ 89%] Linking CXX executable showtree cd /build/prime-phylo-q2I051/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 [ 90%] Linking CXX executable primeDLRS cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/showtree.dir/link.d CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 90%] Built target showtree make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 91%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/primeDLRS.dir/link.d CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 91%] Built target primeDLRS make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend [ 92%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o -MF CMakeFiles/reconcile.dir/Rootalyzer.cc.o.d -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc [ 93%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 93%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o -MF CMakeFiles/reroot.dir/reroot.cc.o.d -o CMakeFiles/reroot.dir/reroot.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc:1: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 93%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -MF CMakeFiles/reconcile.dir/reconcile.cc.o.d -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:10: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:14: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function ‘int main(int, char**)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value ‘input_format__NULL’ not handled in switch [-Wswitch] 76 | switch(args_info.input_format_arg) | ^ /build/prime-phylo-q2I051/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) { | ^ [ 94%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o -MF CMakeFiles/reroot.dir/cmdline.c.o.d -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.c In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:14: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function ‘int main(int, char**)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 37 | char *ofilename = "mpr.out"; | ^~~~~~~~~ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 128 | catch (AnError e) { | ^ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function ‘void populateGsMap(beep::Tree, beep::StrStrMap&)’: /build/prime-phylo-q2I051/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable reroot cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/reroot.dir/link.d CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 95%] Built target reroot make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 95%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 96%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -MF CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o.d -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc [ 97%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o -MF CMakeFiles/reconcile.dir/cmdline.c.o.d -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.c [ 97%] Linking CXX executable reconcile cd /build/prime-phylo-q2I051/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 In file included from /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:7: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:9: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function ‘int main(int, char**)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value ‘input_format__NULL’ not handled in switch [-Wswitch] 51 | switch(args_info.input_format_arg) | ^ /build/prime-phylo-q2I051/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) { | ^ [ 98%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -MF CMakeFiles/tree2leafnames.dir/cmdline.c.o.d -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/reconcile.dir/link.d CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 98%] Built target reconcile make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 98%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-q2I051/prime-phylo-1.0.11 /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build make[3]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 99%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o -MF CMakeFiles/chainsaw.dir/chainsaw.cc.o.d -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc [ 99%] Linking CXX executable tree2leafnames cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/tree2leafnames.dir/link.d CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 99%] Built target tree2leafnames [ 99%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o cd /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-q2I051/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/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value ‘guest_tree_format__NULL’ not handled in switch [-Wswitch] 90 | switch(ai.guest_tree_format_arg) | ^ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘beep::Tree ReadHostTree(gengetopt_args_info&)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:114:9: warning: enumeration value ‘host_tree_format__NULL’ not handled in switch [-Wswitch] 114 | switch(ai.host_tree_format_arg) | ^ /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘int main(int, char**)’: /build/prime-phylo-q2I051/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:163:24: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 163 | catch (AnError e) { | ^ /build/prime-phylo-q2I051/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) { | ^ [100%] Linking CXX executable chainsaw cd /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-q2I051/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,--dependency-file=CMakeFiles/chainsaw.dir/link.d CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [100%] Built target chainsaw make[2]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/prime-phylo-q2I051/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 -j2 install DESTDIR=/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-q2I051/prime-phylo-1.0.11 -B/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Debug" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/chainsaw.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDLRS.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeGEM.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reconcile.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reroot.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/showtree.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/treesize.1 -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw -- Set non-toolchain portion of runtime path of "/build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-q2I051/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/mcmc_analysis make[1]: Leaving directory '/build/prime-phylo-q2I051/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/prime-phylo-q2I051/prime-phylo-1.0.11' dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so make[1]: Leaving directory '/build/prime-phylo-q2I051/prime-phylo-1.0.11' dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-13_amd64.deb'. dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-13_amd64.deb'. dpkg-genbuildinfo -O../prime-phylo_1.0.11-13_amd64.buildinfo dpkg-genchanges -O../prime-phylo_1.0.11-13_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-01-22T09:35:45Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 22 Jan 2025 09:35:45 +0000 | +------------------------------------------------------------------------------+ prime-phylo_1.0.11-13_amd64.changes: ------------------------------------ Format: 1.8 Date: Sun, 03 Nov 2024 14:11:50 +0100 Source: prime-phylo Binary: prime-phylo prime-phylo-dbgsym Architecture: source amd64 Version: 1.0.11-13 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: prime-phylo - bayesian estimation of gene trees taking the species tree into ac Closes: 1086370 Changes: prime-phylo (1.0.11-13) unstable; urgency=medium . * openmpi5.patch: new: fix build failure with openmpi 5. (Closes: #1086370) * d/lintian-overrides: flag rpath, needed for openmpi. * d/salsa-ci.yml: disable i386 CI build. Checksums-Sha1: 037611f630bf05a1a3100c5cab8c208fdef0529b 1335 prime-phylo_1.0.11-13.dsc f1b3cbd2c2e77d9f0074cf8596174bc812eee2c0 11008 prime-phylo_1.0.11-13.debian.tar.xz 00241fd244a22764f8bdaade13a7adbac63c4503 10068532 prime-phylo-dbgsym_1.0.11-13_amd64.deb 741a4339f78945ad29dd413efd64d56efd630e15 10835 prime-phylo_1.0.11-13_amd64.buildinfo 6854af76b65c203fc88c8ebde6a87def0354a762 843996 prime-phylo_1.0.11-13_amd64.deb Checksums-Sha256: c52d177f1946d8240927448c9e2c5b6e288b15b2dd4658a7c325bdbc0afaa9f6 1335 prime-phylo_1.0.11-13.dsc 81d2a589126ef6b2eb922dd5606724202e526a9158591b2bef55481777bc2a32 11008 prime-phylo_1.0.11-13.debian.tar.xz af1738e774594b8a7a02496a298f1191f77572bf431f3856b2d6ef690c4fac46 10068532 prime-phylo-dbgsym_1.0.11-13_amd64.deb 63e8962d10b879eac411dc0175414b3ddec910492a272b29d83f170973b9c0d1 10835 prime-phylo_1.0.11-13_amd64.buildinfo 1fc1ac0bfa78a21a0c9ffd073bdcfae88c51b245b76db42b383354cbfc6d6a17 843996 prime-phylo_1.0.11-13_amd64.deb Files: 5b68087217182c2e54633062d316216a 1335 science optional prime-phylo_1.0.11-13.dsc a2c4542421bb0b4559db1b1697e17323 11008 science optional prime-phylo_1.0.11-13.debian.tar.xz d34242fbe073debfbef7b4cfd3e5cb74 10068532 debug optional prime-phylo-dbgsym_1.0.11-13_amd64.deb d92fb453ff809e823943dca0556d92dd 10835 science optional prime-phylo_1.0.11-13_amd64.buildinfo e3710b019c81d2389b788e05a324b153 843996 science optional prime-phylo_1.0.11-13_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Wed, 22 Jan 2025 09:35:45 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: prime-phylo Binary: prime-phylo prime-phylo-dbgsym Architecture: amd64 source Version: 1.0.11-13 Checksums-Md5: 5b68087217182c2e54633062d316216a 1335 prime-phylo_1.0.11-13.dsc d34242fbe073debfbef7b4cfd3e5cb74 10068532 prime-phylo-dbgsym_1.0.11-13_amd64.deb e3710b019c81d2389b788e05a324b153 843996 prime-phylo_1.0.11-13_amd64.deb Checksums-Sha1: 037611f630bf05a1a3100c5cab8c208fdef0529b 1335 prime-phylo_1.0.11-13.dsc 00241fd244a22764f8bdaade13a7adbac63c4503 10068532 prime-phylo-dbgsym_1.0.11-13_amd64.deb 6854af76b65c203fc88c8ebde6a87def0354a762 843996 prime-phylo_1.0.11-13_amd64.deb Checksums-Sha256: c52d177f1946d8240927448c9e2c5b6e288b15b2dd4658a7c325bdbc0afaa9f6 1335 prime-phylo_1.0.11-13.dsc af1738e774594b8a7a02496a298f1191f77572bf431f3856b2d6ef690c4fac46 10068532 prime-phylo-dbgsym_1.0.11-13_amd64.deb 1fc1ac0bfa78a21a0c9ffd073bdcfae88c51b245b76db42b383354cbfc6d6a17 843996 prime-phylo_1.0.11-13_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 22 Jan 2025 09:35:44 +0000 Build-Path: /build/prime-phylo-q2I051/prime-phylo-1.0.11 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bison (= 2:3.8.2+dfsg-1+b2), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20241223), cmake (= 3.31.4-2), cmake-data (= 3.31.4-2), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-1), diffutils (= 1:3.10-2), docutils-common (= 0.21.2+dfsg-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), flex (= 2.6.4-8.2+b4), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-12), gcc-13-base (= 13.3.0-12), gcc-13-x86-64-linux-gnu (= 13.3.0-12), gcc-14 (= 14.2.0-14), gcc-14-base (= 14.2.0-14), gcc-14-x86-64-linux-gnu (= 14.2.0-14), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gengetopt (= 2.23+dfsg1-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), gfortran (= 4:14.2.0-1), gfortran-14 (= 14.2.0-14), gfortran-14-x86-64-linux-gnu (= 14.2.0-14), gfortran-x86-64-linux-gnu (= 4:14.2.0-1), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), hostname (= 3.25), ibverbs-providers (= 55.0-1), icu-devtools (= 72.1-6), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b2), libamdhip64-5 (= 5.7.1-5), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.4-1.1), libasan8 (= 14.2.0-14), libatomic1 (= 14.2.0-14), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b1), libbinutils (= 2.43.50.20250108-1), libblas-dev (= 3.12.0-4), libblas3 (= 3.12.0-4), libblkid1 (= 2.40.4-1), libboost-dev (= 1.83.0.2+b2), libboost-mpi-dev (= 1.83.0.2+b2), libboost-mpi1.83-dev (= 1.83.0-4), libboost-mpi1.83.0 (= 1.83.0-4), libboost-serialization-dev (= 1.83.0.2+b2), libboost-serialization1.83-dev (= 1.83.0-4), libboost-serialization1.83.0 (= 1.83.0-4), libboost1.83-dev (= 1.83.0-4), libbrotli1 (= 1.1.0-2+b6), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-5), libc-dev-bin (= 2.40-5), libc6 (= 2.40-5), libc6-dev (= 2.40-5), libcap-ng0 (= 0.8.5-4), libcap2 (= 1:2.66-5+b1), libcbor0.10 (= 0.10.2-2), libcc1-0 (= 14.2.0-14), libcom-err2 (= 1.47.2-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.43.50.20250108-1), libctf0 (= 2.43.50.20250108-1), libcurl4t64 (= 8.11.1-1+b1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.277), libdebhelper-perl (= 13.24.1), libdpkg-perl (= 1.22.14), libdrm-amdgpu1 (= 2.4.123-1), libdrm-common (= 2.4.123-1), libdrm2 (= 2.4.123-1), libedit2 (= 3.1-20250104-1), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-dev (= 2.1.12-stable-10+b1), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.6.4-1), libfabric1 (= 1.17.0-3.1), libffi8 (= 3.4.6-1), libfido2-1 (= 1.15.0-1+b1), libfile-stripnondeterminism-perl (= 1.14.1-1), libgcc-13-dev (= 13.3.0-12), libgcc-14-dev (= 14.2.0-14), libgcc-s1 (= 14.2.0-14), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran-14-dev (= 14.2.0-14), libgfortran5 (= 14.2.0-14), libgmp10 (= 2:6.3.0+dfsg-3), libgnutls30t64 (= 3.8.8-2), libgomp1 (= 14.2.0-14), libgprofng0 (= 2.43.50.20250108-1), libgssapi-krb5-2 (= 1.21.3-4), libhogweed6t64 (= 3.10-1+b1), libhsa-runtime64-1 (= 6.1.2-2), libhsakmt1 (= 6.1.2+ds-1), libhwasan0 (= 14.2.0-14), libhwloc-dev (= 2.11.2-1), libhwloc-plugins (= 2.11.2-1), libhwloc15 (= 2.11.2-1), libibmad5 (= 55.0-1), libibumad3 (= 55.0-1), libibverbs-dev (= 55.0-1), libibverbs1 (= 55.0-1), libicu-dev (= 72.1-6), libicu72 (= 72.1-6), libidn2-0 (= 2.3.7-2+b1), libisl23 (= 0.27-1), libitm1 (= 14.2.0-14), libjansson4 (= 2.14-2+b3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-sphinxdoc (= 8.1.3-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libjsoncpp26 (= 1.9.6-3), libk5crypto3 (= 1.21.3-4), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-4), libkrb5support0 (= 1.21.3-4), liblapack-dev (= 3.12.0-4), liblapack3 (= 3.12.0-4), libldap2 (= 2.6.9+dfsg-1), libllvm17t64 (= 1:17.0.6-20+b1), liblsan0 (= 14.2.0-14), libltdl-dev (= 2.5.4-2), libltdl7 (= 2.5.4-2), liblz4-1 (= 1.9.4-4), liblzma5 (= 5.6.3-1+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.40.4-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libmunge2 (= 0.5.15-4+b1), libncursesw6 (= 6.5-2+b1), libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libnl-3-200 (= 3.7.0-0.3+b1), libnl-3-dev (= 3.7.0-0.3+b1), libnl-route-3-200 (= 3.7.0-0.3+b1), libnl-route-3-dev (= 3.7.0-0.3+b1), libnuma-dev (= 2.0.18-1+b1), libnuma1 (= 2.0.18-1+b1), libopenmpi-dev (= 5.0.6-3), libopenmpi40 (= 5.0.6-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libpciaccess0 (= 0.17-3+b3), libpcre2-8-0 (= 10.44-5), libperl5.40 (= 5.40.1-1), libpipeline1 (= 1.5.8-1), libpmix-dev (= 5.0.6-1), libpmix2t64 (= 5.0.6-1), libproc2-0 (= 2:4.0.4-6), libpsl5t64 (= 0.21.2-1.1+b1), libpsm-infinipath1 (= 3.3+20.604758e7-6.3), libpsm2-2 (= 11.2.185-2.1), libpython3-stdlib (= 3.13.1-2), libpython3.13-minimal (= 3.13.1-3), libpython3.13-stdlib (= 3.13.1-3), libquadmath0 (= 14.2.0-14), librdmacm1t64 (= 55.0-1), libreadline8t64 (= 8.2-6), librhash1 (= 1.4.5-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8+b1), libsasl2-modules-db (= 2.1.28+dfsg1-8+b1), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsemanage-common (= 3.7-2), libsemanage2 (= 3.7-2+b1), libsepol2 (= 3.7-1), libsframe1 (= 2.43.50.20250108-1), libsmartcols1 (= 2.40.4-1), libsqlite3-0 (= 3.46.1-1), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.4.0-2), libstdc++-14-dev (= 14.2.0-14), libstdc++6 (= 14.2.0-14), libsystemd0 (= 257.2-2), libtasn1-6 (= 4.19.0-3+b3), libtinfo6 (= 6.5-2+b1), libtool (= 2.5.4-2), libtsan2 (= 14.2.0-14), libubsan1 (= 14.2.0-14), libuchardet0 (= 0.0.8-1+b2), libucx0 (= 1.17.0+ds-3), libudev1 (= 257.2-2), libunistring5 (= 1.3-1), libuuid1 (= 2.40.4-1), libuv1t64 (= 1.48.0-7), libx11-6 (= 2:1.8.10-2), libx11-data (= 2:1.8.10-2), libxau6 (= 1:1.0.11-1), libxcb1 (= 1.17.0-2+b1), libxdmcp6 (= 1:1.1.5-1), libxext6 (= 2:1.3.4-1+b3), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxml2-dev (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxnvctrl0 (= 535.171.04-1+b1), libxxhash0 (= 0.8.3-2), libz3-4 (= 4.13.3-1), libzstd1 (= 1.5.6+dfsg-2), linux-libc-dev (= 6.12.10-1), login.defs (= 1:4.16.0-7), m4 (= 1.4.19-5), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), mpi-default-dev (= 1.18), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), netbase (= 6.4), ocl-icd-libopencl1 (= 2.3.2-1+b2), openmpi-bin (= 5.0.6-3), openmpi-common (= 5.0.6-3), openssh-client (= 1:9.9p1-3), openssl (= 3.4.0-2), openssl-provider-legacy (= 3.4.0-2), passwd (= 1:4.16.0-7), patch (= 2.7.6-7), perl (= 5.40.1-1), perl-base (= 5.40.1-1), perl-modules-5.40 (= 5.40.1-1), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-6), python-babel-localedata (= 2.16.0-1), python3 (= 3.13.1-2), python3-alabaster (= 0.7.16-0.1), python3-autocommand (= 2.2.2-3), python3-babel (= 2.16.0-1), python3-certifi (= 2024.12.14+ds-1), python3-chardet (= 5.2.0+dfsg-2), python3-charset-normalizer (= 3.4.0-1+b1), python3-defusedxml (= 0.7.1-3), python3-docutils (= 0.21.2+dfsg-2), python3-idna (= 3.8-2), python3-imagesize (= 1.4.1-1), python3-inflect (= 7.3.1-2), python3-jaraco.context (= 6.0.0-1), python3-jaraco.functools (= 4.1.0-1), python3-jinja2 (= 3.1.3-2), python3-markupsafe (= 2.1.5-1+b2), python3-minimal (= 3.13.1-2), python3-more-itertools (= 10.6.0-1), python3-packaging (= 24.2-1), python3-pkg-resources (= 75.6.0-1), python3-pygments (= 2.18.0+dfsg-2), python3-requests (= 2.32.3+dfsg-1), python3-roman (= 4.2-1), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 8.1.3-4), python3-typeguard (= 4.4.1-1), python3-typing-extensions (= 4.12.2-2), python3-urllib3 (= 2.3.0-1), python3.13 (= 3.13.1-3), python3.13-minimal (= 3.13.1-3), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sgml-base (= 1.31), sphinx-common (= 8.1.3-4), sysvinit-utils (= 3.13-1), tar (= 1.35+dfsg-3.1), tzdata (= 2025a-1), util-linux (= 2.40.4-1), xml-core (= 0.19), xz-utils (= 5.6.3-1+b1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1730639510" +------------------------------------------------------------------------------+ | Package contents Wed, 22 Jan 2025 09:35:45 +0000 | +------------------------------------------------------------------------------+ prime-phylo-dbgsym_1.0.11-13_amd64.deb -------------------------------------- new Debian package, version 2.0. size 10068532 bytes: control archive=1096 bytes. 802 bytes, 12 lines control 1254 bytes, 12 lines md5sums Package: prime-phylo-dbgsym Source: prime-phylo Version: 1.0.11-13 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 10560 Depends: prime-phylo (= 1.0.11-13) Section: debug Priority: optional Description: debug symbols for prime-phylo Build-Ids: 006584e2519e853391532bb6556dfd449ad56271 6377efbee4d02c3805a6ca3a7967e92e10e20053 97ddffa16bb6841d86fc2c677da385d649982491 9f76613b38e1f87a0907c9a2a0be265e1741d36b b851a08121050352bd0136fa21da9e7551194921 c360ebeb5f55b9369e4bc4173820e97f92b12050 c6302aa04c051da387f23a4567df74224128a003 d8f794385b01ce29449b95fbb056d1acb95250e9 f05d567a9165e966375b9974dd8cdac59d17cd04 f140b637a240585dc9e1f9106bf4c972896174e5 fdbd17cdfca6de9a5760e059353cf6a47cbb225d drwxr-xr-x root/root 0 2024-11-03 13:11 ./ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/00/ -rw-r--r-- root/root 43200 2024-11-03 13:11 ./usr/lib/debug/.build-id/00/6584e2519e853391532bb6556dfd449ad56271.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/63/ -rw-r--r-- root/root 75320 2024-11-03 13:11 ./usr/lib/debug/.build-id/63/77efbee4d02c3805a6ca3a7967e92e10e20053.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/97/ -rw-r--r-- root/root 87144 2024-11-03 13:11 ./usr/lib/debug/.build-id/97/ddffa16bb6841d86fc2c677da385d649982491.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/9f/ -rw-r--r-- root/root 128832 2024-11-03 13:11 ./usr/lib/debug/.build-id/9f/76613b38e1f87a0907c9a2a0be265e1741d36b.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/b8/ -rw-r--r-- root/root 44104 2024-11-03 13:11 ./usr/lib/debug/.build-id/b8/51a08121050352bd0136fa21da9e7551194921.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/c3/ -rw-r--r-- root/root 9441848 2024-11-03 13:11 ./usr/lib/debug/.build-id/c3/60ebeb5f55b9369e4bc4173820e97f92b12050.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/c6/ -rw-r--r-- root/root 61992 2024-11-03 13:11 ./usr/lib/debug/.build-id/c6/302aa04c051da387f23a4567df74224128a003.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/d8/ -rw-r--r-- root/root 41888 2024-11-03 13:11 ./usr/lib/debug/.build-id/d8/f794385b01ce29449b95fbb056d1acb95250e9.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/f0/ -rw-r--r-- root/root 304112 2024-11-03 13:11 ./usr/lib/debug/.build-id/f0/5d567a9165e966375b9974dd8cdac59d17cd04.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/f1/ -rw-r--r-- root/root 161016 2024-11-03 13:11 ./usr/lib/debug/.build-id/f1/40b637a240585dc9e1f9106bf4c972896174e5.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.build-id/fd/ -rw-r--r-- root/root 277904 2024-11-03 13:11 ./usr/lib/debug/.build-id/fd/bd17cdfca6de9a5760e059353cf6a47cbb225d.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 117232 2024-11-03 13:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/prime-phylo.debug drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-11-03 13:11 ./usr/share/doc/prime-phylo-dbgsym -> prime-phylo prime-phylo_1.0.11-13_amd64.deb ------------------------------- new Debian package, version 2.0. size 843996 bytes: control archive=1824 bytes. 1088 bytes, 19 lines control 2172 bytes, 33 lines md5sums Package: prime-phylo Version: 1.0.11-13 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3159 Depends: perl:any, libblas3 | libblas.so.3, libboost-mpi1.83.0 (>= 1.83.0), libboost-serialization1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), liblapack3 | liblapack.so.3, libopenmpi40 (>= 5.0.6), libstdc++6 (>= 14), libxml2 (>= 2.7.4) Suggests: njplot, treeviewx, muscle, probalign, mafft, python3-biopython, mrbayes, phyml, raxml Section: science Priority: optional Homepage: http://prime.sbc.su.se Description: bayesian estimation of gene trees taking the species tree into account PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. . The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format. drwxr-xr-x root/root 0 2024-11-03 13:11 ./ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/bin/ -rwxr-xr-x root/root 43800 2024-11-03 13:11 ./usr/bin/chainsaw -rwxr-xr-x root/root 33128 2012-12-17 15:52 ./usr/bin/mcmc_analysis -rwxr-xr-x root/root 113056 2024-11-03 13:11 ./usr/bin/primeDLRS -rwxr-xr-x root/root 117152 2024-11-03 13:11 ./usr/bin/primeDTLSR -rwxr-xr-x root/root 48440 2024-11-03 13:11 ./usr/bin/primeGEM lrwxrwxrwx root/root 0 2024-11-03 13:11 ./usr/bin/primeGSRf -> primeDLRS -rwxr-xr-x root/root 51872 2024-11-03 13:11 ./usr/bin/reconcile -rwxr-xr-x root/root 60280 2024-11-03 13:11 ./usr/bin/reroot -rwxr-xr-x root/root 35888 2024-11-03 13:11 ./usr/bin/showtree -rwxr-xr-x root/root 27256 2024-11-03 13:11 ./usr/bin/tree2leafnames -rwxr-xr-x root/root 31392 2024-11-03 13:11 ./usr/bin/treesize drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/lib/prime-phylo/ -rw-r--r-- root/root 55376 2024-11-03 13:11 ./usr/lib/prime-phylo/libprime-phylo-sfile.so -rw-r--r-- root/root 2558328 2024-11-03 13:11 ./usr/lib/prime-phylo/libprime-phylo.so drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/doc/prime-phylo/ -rw-r--r-- root/root 381 2012-12-17 15:52 ./usr/share/doc/prime-phylo/README -rw-r--r-- root/root 532 2024-11-03 13:11 ./usr/share/doc/prime-phylo/README.test -rw-r--r-- root/root 942 2024-11-03 13:11 ./usr/share/doc/prime-phylo/changelog.Debian.gz -rw-r--r-- root/root 505 2012-12-17 15:52 ./usr/share/doc/prime-phylo/changelog.gz -rw-r--r-- root/root 7287 2024-11-03 13:11 ./usr/share/doc/prime-phylo/copyright drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/doc/prime-phylo/examples/ -rw-r--r-- root/root 393 2024-11-03 13:11 ./usr/share/doc/prime-phylo/examples/gse -rw-r--r-- root/root 162 2024-11-03 13:11 ./usr/share/doc/prime-phylo/examples/hostfile -rw-r--r-- root/root 3513 2024-11-03 13:11 ./usr/share/doc/prime-phylo/examples/seqfile -rw-r--r-- root/root 14 2024-11-03 13:11 ./usr/share/doc/prime-phylo/examples/treefile -rw-r--r-- root/root 974 2024-11-03 13:11 ./usr/share/doc/prime-phylo/run-unit-test drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 699 2024-11-03 13:11 ./usr/share/lintian/overrides/prime-phylo drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/man/ drwxr-xr-x root/root 0 2024-11-03 13:11 ./usr/share/man/man1/ -rw-r--r-- root/root 653 2024-11-03 13:11 ./usr/share/man/man1/chainsaw.1.gz -rw-r--r-- root/root 1284 2024-11-03 13:11 ./usr/share/man/man1/mcmc_analysis.1.gz -rw-r--r-- root/root 2154 2024-11-03 13:11 ./usr/share/man/man1/primeDLRS.1.gz -rw-r--r-- root/root 1992 2024-11-03 13:11 ./usr/share/man/man1/primeDTLSR.1.gz -rw-r--r-- root/root 987 2024-11-03 13:11 ./usr/share/man/man1/primeGEM.1.gz lrwxrwxrwx root/root 0 2024-11-03 13:11 ./usr/share/man/man1/primeGSRf.1.gz -> primeDLRS.1.gz -rw-r--r-- root/root 654 2024-11-03 13:11 ./usr/share/man/man1/reconcile.1.gz -rw-r--r-- root/root 886 2024-11-03 13:11 ./usr/share/man/man1/reroot.1.gz -rw-r--r-- root/root 904 2024-11-03 13:11 ./usr/share/man/man1/showtree.1.gz -rw-r--r-- root/root 494 2024-11-03 13:11 ./usr/share/man/man1/tree2leafnames.1.gz -rw-r--r-- root/root 608 2024-11-03 13:11 ./usr/share/man/man1/treesize.1.gz +------------------------------------------------------------------------------+ | Post Build Wed, 22 Jan 2025 09:35:45 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 22 Jan 2025 09:35:45 +0000 | +------------------------------------------------------------------------------+ Purging /build/prime-phylo-q2I051 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 22 Jan 2025 09:35:47 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 164096 Build-Time: 198 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 29 Job: /srv/debomatic/incoming/prime-phylo_1.0.11-13.dsc Machine Architecture: amd64 Package: prime-phylo Package-Time: 238 Source-Version: 1.0.11-13 Space: 164096 Status: successful Version: 1.0.11-13 -------------------------------------------------------------------------------- Finished at 2025-01-22T09:35:45Z Build needed 00:03:58, 164096k disk space