sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | prime-phylo 1.0.11-14 (amd64) Sun, 12 Jul 2026 05:31:10 +0000 | +==============================================================================+ Package: prime-phylo Version: 1.0.11-14 Source Version: 1.0.11-14 Distribution: perl-5.44-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 Sun, 12 Jul 2026 05:31:11 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup prime-phylo_1.0.11-14 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup prime-phylo_1.0.11-14 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 12 Jul 2026 05:31:11 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:3 http://deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sun, 12 Jul 2026 05:31:13 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/prime-phylo_1.0.11-14.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 12 Jul 2026 05:31:13 +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-cDBuCy/resolver-IOz5P1/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/prime-phylo-cDBuCy/resolver-IOz5P1/apt_archive ./ InRelease Get:2 copy:/build/prime-phylo-cDBuCy/resolver-IOz5P1/apt_archive ./ Release [609 B] Ign:3 copy:/build/prime-phylo-cDBuCy/resolver-IOz5P1/apt_archive ./ Release.gpg Get:4 copy:/build/prime-phylo-cDBuCy/resolver-IOz5P1/apt_archive ./ Sources [770 B] Get:5 copy:/build/prime-phylo-cDBuCy/resolver-IOz5P1/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... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bison bsdextrautils cmake debhelper dh-autoreconf dh-strip-nondeterminism dwz file flex gengetopt gettext gettext-base gfortran gfortran-15 gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-container1.90-dev libboost-container1.90.0 libboost-dev libboost-exception1.90-dev libboost-graph1.90-dev libboost-graph1.90.0 libboost-mpi-dev libboost-mpi1.90-dev libboost-mpi1.90.0 libboost-regex1.90-dev libboost-regex1.90.0 libboost-serialization-dev libboost-serialization1.90-dev libboost-serialization1.90.0 libboost-test1.90-dev libboost-test1.90.0 libboost1.90-dev libbrotli1 libbsd0 libcbor0.10 libclang-common-21-dev 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 libfuse3-4 libgfortran-15-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm21 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpmix2t64 libproc2-1 libprrte-bin libprrte-dev libprrte3 libpsl5t64 libpsm2-2 librdmacm1t64 librhash1 libssh2-1t64 libtool libucc1 libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxml2-dev libxnvctrl0 libz3-4 libze1 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssh-common pci.ids po-debconf procps sensible-utils 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 gnulib-l10n gfortran-multilib gfortran-doc gfortran-15-multilib gfortran-15-doc libcoarrays-dev groff lrzip liblapack-doc libboost-doc graphviz libboost1.90-doc libboost-atomic1.90-dev libboost-chrono1.90-dev libboost-context1.90-dev libboost-contract1.90-dev libboost-coroutine1.90-dev libboost-date-time1.90-dev libboost-fiber1.90-dev libboost-filesystem1.90-dev libboost-graph-parallel1.90-dev libboost-iostreams1.90-dev libboost-json1.90-dev libboost-locale1.90-dev libboost-log1.90-dev libboost-math1.90-dev libboost-mpi-python1.90-dev libboost-nowide1.90-dev libboost-numpy1.90-dev libboost-program-options1.90-dev libboost-python1.90-dev libboost-random1.90-dev libboost-stacktrace1.90-dev libboost-thread1.90-dev libboost-timer1.90-dev libboost-type-erasure1.90-dev libboost-url1.90-dev libboost-wave1.90-dev libboost1.90-tools-dev libmpfrc++-dev libntl-dev fuse3 krb5-doc krb5-user libhwloc-contrib-plugins libjs-jquery-ui-docs libtool-doc liblzma-doc openmpi-doc pkgconf m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: libfl-dev curl | wget | lynx python3:any libclang-rt-21-dev ca-certificates libarchive-cpio-perl javascript-common krb5-locales libcoarrays-openmpi-dev libpmix-dev publicsuffix xauth libmail-sendmail-perl psmisc linux-sysctl-defaults The following NEW packages will be installed: autoconf automake autopoint autotools-dev bison bsdextrautils cmake debhelper dh-autoreconf dh-strip-nondeterminism dwz file flex gengetopt gettext gettext-base gfortran gfortran-15 gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-container1.90-dev libboost-container1.90.0 libboost-dev libboost-exception1.90-dev libboost-graph1.90-dev libboost-graph1.90.0 libboost-mpi-dev libboost-mpi1.90-dev libboost-mpi1.90.0 libboost-regex1.90-dev libboost-regex1.90.0 libboost-serialization-dev libboost-serialization1.90-dev libboost-serialization1.90.0 libboost-test1.90-dev libboost-test1.90.0 libboost1.90-dev libbrotli1 libbsd0 libcbor0.10 libclang-common-21-dev 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 libfuse3-4 libgfortran-15-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm21 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpmix2t64 libproc2-1 libprrte-bin libprrte-dev libprrte3 libpsl5t64 libpsm2-2 librdmacm1t64 librhash1 libssh2-1t64 libtool libucc1 libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxml2-dev libxnvctrl0 libz3-4 libze1 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssh-common pci.ids po-debconf procps sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 150 newly installed, 0 to remove and 0 not upgraded. Need to get 155 MB of archives. After this operation, 769 MB of additional disk space will be used. Get:1 copy:/build/prime-phylo-cDBuCy/resolver-IOz5P1/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [936 B] Get:2 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b5 [425 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libproc2-1 amd64 2:4.0.6-2 [69.2 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.6-2 [983 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.1+b1 [28.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.17.0-1 [80.6 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 openssh-common amd64 1:10.4p1-1 [481 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-3 [132 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20260512-1 [93.6 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:26 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.4p1-1 [720 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b3 [1170 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.8.8-2 [362 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.22.1-1 [23.3 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.21.0-2 [422 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.8-1 [87.3 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1.1+b1 [135 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.52.1-4 [158 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.3.4-1 [16.2 MB] Get:48 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:54 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 gengetopt amd64 2.23+dfsg1-1 [173 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.1.0-2 [877 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.3.0-1 [877 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.3.0-1 [12.8 MB] Get:64 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.3.0-1 [22.2 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-5+b1 [1284 B] Get:66 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:15.2.0-5+b1 [1440 B] Get:67 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2+b1 [62.2 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2+b1 [200 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 63.0-2 [62.8 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 63.0-2 [383 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1.1 [8644 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b4 [28.2 MB] Get:73 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7+b4 [768 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Get:75 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-3 [7860 B] Get:76 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-3 [38.5 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-3 [23.3 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b2 [22.0 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-8 [206 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-8 [219 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-6 [11.3 MB] Get:84 http://deb.debian.org/debian unstable/main amd64 libboost-container1.90.0 amd64 1.90.0-6 [252 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libboost-container1.90-dev amd64 1.90.0-6 [257 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.90.0.2 [3064 B] Get:87 http://deb.debian.org/debian unstable/main amd64 libboost-exception1.90-dev amd64 1.90.0-6 [222 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.90.0 amd64 1.90.0-6 [355 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.90.0 amd64 1.90.0-6 [327 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.90-dev amd64 1.90.0-6 [343 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.90.0 amd64 1.90.0-6 [326 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.90-dev amd64 1.90.0-6 [364 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libboost-test1.90.0 amd64 1.90.0-6 [465 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libboost-test1.90-dev amd64 1.90.0-6 [533 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.90-dev amd64 1.90.0-6 [378 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.13-stable-1 [133 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.13-stable-1 [53.8 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 63.0-2 [71.8 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b2 [716 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.14.0-2 [166 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.18-1 [18.8 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 pci.ids all 0.0~2026.07.06-1 [285 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.19-2 [18.5 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.28.2-2 [795 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1+b1 [42.8 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.14.0-2 [21.7 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3+b2 [670 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.2-2 [103 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 63.0-2 [28.5 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 63.0-2 [43.2 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.22.0~rc1-1 [1015 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.8.0-2 [345 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.10-1 [2018 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.90.0 amd64 1.90.0-6 [263 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2+b1 [105 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2+b1 [220 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 63.0-2 [695 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libprrte3 amd64 3.0.13-3 [451 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-3 [3654 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1+b2 [36.2 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-11 [416 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-11 [168 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.14.0-2 [260 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.13-stable-1 [108 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.13-stable-1 [60.9 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.13-stable-1 [307 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 libprrte-bin amd64 3.0.13-3 [51.9 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.10-1 [1028 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.20 [3504 B] Get:144 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.90-dev amd64 1.90.0-6 [282 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-dev amd64 1.90.0.2 [2940 B] Get:146 http://deb.debian.org/debian unstable/main amd64 libboost-serialization-dev amd64 1.90.0.2 [3088 B] Get:147 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-8 [2548 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-8 [5230 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.15.3+dfsg-1 [746 kB] Preconfiguring packages ... Fetched 155 MB in 1s (164 MB/s) Selecting previously unselected package m4. (Reading database ... 15696 files and directories currently installed.) Preparing to unpack .../000-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package flex. Preparing to unpack .../001-flex_2.6.4-8.2+b5_amd64.deb ... Unpacking flex (2.6.4-8.2+b5) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../002-libexpat1_2.8.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.2-1) ... Selecting previously unselected package libproc2-1:amd64. Preparing to unpack .../003-libproc2-1_2%3a4.0.6-2_amd64.deb ... Unpacking libproc2-1:amd64 (2:4.0.6-2) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.6-2_amd64.deb ... Unpacking procps (2:4.0.6-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... 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Setting up libtool (2.5.4-11) ... Setting up openssh-common (1:10.4p1-1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.13-stable-1) ... Setting up libedit2:amd64 (3.1-20260512-1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.13-stable-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b4) ... Setting up libgfortran-15-dev:amd64 (15.3.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.19-1+b2) ... Setting up libnl-route-3-200:amd64 (3.12.0-2+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b3) ... Setting up dh-autoreconf (22) ... Setting up libboost-container1.90-dev:amd64 (1.90.0-6) ... Setting up libltdl-dev:amd64 (2.5.4-11) ... Setting up libxml2-dev:amd64 (2.15.3+dfsg-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm21:amd64 (1:21.1.8-7+b4) ... Setting up liblapack-dev:amd64 (3.12.1-8) ... 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 (1.22.1-3) ... Setting up libboost-serialization-dev:amd64 (1.90.0.2) ... Setting up libngtcp2-crypto-ossl0:amd64 (1.22.1-1) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.13-stable-1) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up libboost-exception1.90-dev:amd64 (1.90.0-6) ... Setting up libdrm2:amd64 (2.4.134-3) ... Setting up libnl-3-dev:amd64 (3.12.0-2+b1) ... Setting up libboost-regex1.90-dev:amd64 (1.90.0-6) ... Setting up groff-base (1.24.1-1) ... Setting up libamd-comgr3:amd64 (7.0.2+dfsg-3) ... Setting up libhwloc-dev:amd64 (2.14.0-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.134-3) ... Setting up libboost-test1.90-dev:amd64 (1.90.0-6) ... Setting up gfortran-15-x86-64-linux-gnu (15.3.0-1) ... Setting up libibverbs1:amd64 (63.0-2) ... Creating group 'rdma' with GID 993. Setting up libcurl4t64:amd64 (8.21.0-2) ... Setting up ibverbs-providers:amd64 (63.0-2) ... Setting up openssh-client (1:10.4p1-1) ... Created symlink '/etc/systemd/user/sockets.target.wants/ssh-agent.socket' → '/usr/lib/systemd/user/ssh-agent.socket'. Setting up po-debconf (1.0.22) ... Setting up libhwloc-plugins:amd64 (2.14.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up gfortran-x86-64-linux-gnu (4:15.2.0-5+b1) ... Setting up libnl-route-3-dev:amd64 (3.12.0-2+b1) ... Setting up libevent-dev (2.1.13-stable-1) ... Setting up libpmix2t64:amd64 (6.0.0+really5.0.9-3+b2) ... Setting up libboost-graph1.90-dev:amd64 (1.90.0-6) ... Setting up libhsa-runtime64-1:amd64 (6.4.3+dfsg-5) ... Setting up cmake (4.3.4-1) ... Setting up librdmacm1t64:amd64 (63.0-2) ... Setting up gfortran-15 (15.3.0-1) ... Setting up libfabric1:amd64 (2.1.0-1.1+b2) ... Setting up debhelper (14.3) ... Setting up libibverbs-dev:amd64 (63.0-2) ... Setting up gfortran (4:15.2.0-5+b1) ... 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 libamdhip64-6:amd64 (6.4.3-5) ... Setting up libprrte3:amd64 (3.0.13-3) ... Setting up libprrte-dev:amd64 (3.0.13-3) ... Setting up libprrte-bin (3.0.13-3) ... Setting up libucx0:amd64 (1.22.0~rc1-1) ... Setting up libucc1:amd64 (1.8.0-2) ... Setting up libopenmpi40:amd64 (5.0.10-1) ... Setting up libboost-mpi1.90.0 (1.90.0-6) ... Setting up openmpi-bin (5.0.10-1) ... 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) does not exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev (5.0.10-1) ... 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 (1.20) ... Setting up libboost-mpi1.90-dev (1.90.0-6) ... Setting up libboost-mpi-dev (1.90.0.2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 12 Jul 2026 05:31:29 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 12 Jul 2026 05:31:29 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bison_2:3.8.2+dfsg-1+b3 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 cmake_4.3.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 flex_2.6.4-8.2+b5 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gengetopt_2.23+dfsg1-1 gettext_1.0-3 gettext-base_1.0-3 gfortran_4:15.2.0-5+b1 gfortran-15_15.3.0-1 gfortran-15-x86-64-linux-gnu_15.3.0-1 gfortran-x86-64-linux-gnu_4:15.2.0-5+b1 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7 gpg-agent_2.4.9-7 gpgconf_2.4.9-7 gpgsm_2.4.9-7 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 ibverbs-providers_63.0-2 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.8-2 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblas-dev_3.12.1-8 libblas3_3.12.1-8 libblkid1_2.42.2-1 libboost-container1.90-dev_1.90.0-6 libboost-container1.90.0_1.90.0-6 libboost-dev_1.90.0.2 libboost-exception1.90-dev_1.90.0-6 libboost-graph1.90-dev_1.90.0-6 libboost-graph1.90.0_1.90.0-6 libboost-mpi-dev_1.90.0.2 libboost-mpi1.90-dev_1.90.0-6 libboost-mpi1.90.0_1.90.0-6 libboost-regex1.90-dev_1.90.0-6 libboost-regex1.90.0_1.90.0-6 libboost-serialization-dev_1.90.0.2 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tar_1.35+dfsg-4 tpm-udev_4.1.3-6 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 12 Jul 2026 05:31:29 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prime-phylo Binary: prime-phylo Architecture: any Version: 1.0.11-14 Maintainer: Debian Med Packaging Team Uploaders: Erik Sjolund , Andreas Tille , Étienne Mollier Homepage: http://prime.sbc.su.se Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev Package-List: prime-phylo deb science optional arch=any Checksums-Sha1: 1dd3b086599e29f6a17319f8ebe294cd6eed0c07 750651 prime-phylo_1.0.11.orig.tar.gz b8326a68e71693ad10cc837354f99cf221ab06ca 11760 prime-phylo_1.0.11-14.debian.tar.xz Checksums-Sha256: 5d46b4e528417bb4a0be56756069f255f86ab58b28b55fa6a96983f10585bd8d 750651 prime-phylo_1.0.11.orig.tar.gz a04cc5fe6f55536ac181904cbb0bba934c0dec125a4ebf3d2affcd5a65b42647 11760 prime-phylo_1.0.11-14.debian.tar.xz Files: 0356071434de01edf92a1b9182ed6ef1 750651 prime-phylo_1.0.11.orig.tar.gz 54305fccaa20abf04f51a910774f38bf 11760 prime-phylo_1.0.11-14.debian.tar.xz Dgit: 9132334739cc6521dd131fc532c93e06f277487c debian archive/debian/1.0.11-14 https://git.dgit.debian.org/prime-phylo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmjRqo4UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrWKg/5AX5J1t72FB8u9G3lSoatmiBdj9Fq zUiUJDSZsTGk9EX+ShTLZTIGhbWo+hR2xfmvGrZbv0ASAhESGsIC05FL0BW4TOsK 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absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting prime-phylo in /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-14.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-Boost160.patch dpkg-source: info: applying fix-gcc-8.patch dpkg-source: info: applying 0003-Fix-build-with-Boost-1.67.patch dpkg-source: info: applying 0004-fix-gcc10-build.patch dpkg-source: info: applying fix-ftbfs-with-gcc13.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying openmpi5.patch dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying cmake-4.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sun, 12 Jul 2026 05:31:30 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network prime-phylo_1.0.11-14 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network prime-phylo_1.0.11-14 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-cDBuCy/prime-phylo-1.0.11 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-30bdcff8-00c9-4587-a401-551ba6746089 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 1.0.11-14 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_1.0.11-14.debian.tar.xz dpkg-source: info: building prime-phylo in ../prime-phylo_1.0.11-14.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-cDBuCy/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 && env -- DEB_PYTHON_INSTALL_LAYOUT=deb --unset=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_C_COMPILER=/usr/bin/x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=/usr/bin/x86_64-linux-gnu-g\+\+ -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. -- The CXX compiler identification is GNU 15.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- The Fortran compiler identification is GNU 15.3.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- The C compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - 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-1.90.0/BoostConfig.cmake (found suitable version "1.90.0", minimum required is "1.40.0") found components: mpi serialization -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.15.3") mpilib is /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi included path is -- Configuring done (3.5s) 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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-cDBuCy/prime-phylo-1.0.11 -B/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/cmake -E make_directory /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile [ 1%] [BISON][MyParser2] Building parser with bison 3.8.2 cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/flex -o/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/cmake -E make_directory /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake "--color=" prime-phylo-sfile make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/x86_64-linux-gnu-gcc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/x86_64-linux-gnu-gcc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_new_sequence’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:35:1: warning: old-style function definition [-Wold-style-definition] 35 | seq_new_sequence(locus, type, definition, length) | ^~~~~~~~~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable ‘date’ set but not used [-Wunused-but-set-variable] 212 | char *top, *date; | ^~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_add_comment’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:288:1: warning: old-style function definition [-Wold-style-definition] 288 | seq_add_comment(e, s) | ^~~~~~~~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_set_definition’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:327:1: warning: old-style function definition [-Wold-style-definition] 327 | seq_set_definition(e, s) | ^~~~~~~~~~~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_set_accession’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:352:1: warning: old-style function definition [-Wold-style-definition] 352 | seq_set_accession(e, s) | ^~~~~~~~~~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_free_comments’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:369:1: warning: old-style function definition [-Wold-style-definition] 369 | seq_free_comments(c) | ^~~~~~~~~~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_free’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:383:1: warning: old-style function definition [-Wold-style-definition] 383 | seq_free(entries) | ^~~~~~~~ [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/x86_64-linux-gnu-gcc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_add_comment’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/x86_64-linux-gnu-gcc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-cDBuCy/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-cDBuCy/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:399:1: warning: old-style function definition [-Wold-style-definition] gb.y:403:9: warning: unused variable ‘new_buf’ [-Wunused-variable] [ 4%] Linking C shared library libprime-phylo-sfile.so cd /build/prime-phylo-cDBuCy/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/x86_64-linux-gnu-gcc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/prime-phylo-cDBuCy/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 -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/prime-phylo-sfile.dir/link.d -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 4%] [BISON][MyParser] Building parser with bison 3.8.2 cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/cmake -E make_directory /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/cmake -E make_directory /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake "--color=" prime-phylo make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 5%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function ‘NHX_debug_print’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function ‘new_annotation’: /build/prime-phylo-cDBuCy/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); | ^ [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/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-cDBuCy/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-cDBuCy/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 *’ /build/prime-phylo-cDBuCy/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-cDBuCy/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 ) | ^~~~~~~ [ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE 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CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscTree.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.hh:1, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:3: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/RandomTreeGenerator.cc [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:6: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function ‘void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function ‘beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector*, beep::StrStrMap*, std::map*, std::map*)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:29: warning: ‘idInt’ may be used uninitialized [-Wmaybe-uninitialized] 1049 | new_node = S.addNode(l, r, idInt, name); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:959:9: note: ‘idInt’ was declared here 959 | int idInt; | ^~~~~ [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:7: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:8: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function ‘void beep::EdgeWeightMCMC::showCurrentTree()’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/prime-phylo-cDBuCy/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$. | ^~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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; | ^~~~~~~~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/prime-phylo-cDBuCy/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/MCMCModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCObject.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: /build/prime-phylo-cDBuCy/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$. | ^~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:6: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:7: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.hh:14, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc [ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.hh:19, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/bits/specfun.h:43, from /usr/include/c++/15/cmath:3913, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/vector:64, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function ‘void beep::EdgeDiscGSR::convertDensitiesToProbabilities()’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:60:18: warning: ‘virtual void beep::ReconciliationModel::setGamma(const beep::GammaMap&)’ was hidden [-Woverloaded-virtual=] 60 | virtual void setGamma(const GammaMap& newGamma); | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:188:10: note: by ‘void beep::EnumerateLabeledReconciliationModel::setGamma(unsigned int)’ 188 | void setGamma(unsigned unique); | ^~~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:9: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/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 | ^~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.hh:8, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:2: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.hh:17: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘unsigned int beep::fastGEM::calcMaxProb(unsigned int)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:136:21: warning: variable ‘topRateProb’ set but not used [-Wunused-but-set-variable] 136 | Probability topRateProb = df->operator()(rate); | ^~~~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printSa()’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLb()’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLt()’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.hh:6, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function ‘void beep::ReconciliationSampler::setAttributesAndProbabilities()’: /build/prime-phylo-cDBuCy/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(); | ^ [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc [ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.hh:16, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function ‘std::string beep::ReconciliationTimeModel::table4os() const’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef ‘MapIter’ locally defined but not used [-Wunused-local-typedefs] 319 | typedef std::map::const_iterator MapIter; | ^~~~~~~ [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.hh:12, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function ‘const std::string beep::ReconciliationTimeSampler::table4os() const’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef ‘MapIter’ locally defined but not used [-Wunused-local-typedefs] 422 | typedef std::map::const_iterator MapIter; | ^~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor ‘beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const std::string&)’: /build/prime-phylo-cDBuCy/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:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:20, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: /build/prime-phylo-cDBuCy/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-cDBuCy/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; | ^~~~~~~~ [ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:22: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:11: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function ‘beep::Tree& beep::HybridTree::getBinaryTree() const’: /build/prime-phylo-cDBuCy/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) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeGenerator.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:58:19: warning: ‘virtual beep::Tree& beep::BirthDeathProbs::getStree() const’ was hidden [-Woverloaded-virtual=] 58 | virtual Tree& getStree() const; | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:40:17: note: by ‘beep::HybridTree& beep::BirthDeathInHybridProbs::getStree()’ 40 | HybridTree& getStree(); | ^~~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:7: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:58:19: warning: ‘virtual beep::Tree& beep::BirthDeathProbs::getStree() const’ was hidden [-Woverloaded-virtual=] 58 | virtual Tree& getStree() const; | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:40:17: note: by ‘beep::HybridTree& beep::BirthDeathInHybridProbs::getStree()’ 40 | HybridTree& getStree(); | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: warning: ‘virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)’ was hidden [-Woverloaded-virtual=] 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); | ^~~~~~~~ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:5: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:4: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:5: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:8: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/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); | ^~~~~~~~ [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:8: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:8: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc In file included from /usr/include/c++/15/ext/hash_map:60, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: /usr/include/c++/15/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:5: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc:2: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SeqIO.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc:8: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:16: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:8: /build/prime-phylo-cDBuCy/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); | ^~~~~~~~ [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function ‘std::map beep::SequenceData::getBaseFrequencies()’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor ‘beep::LA_Matrix::LA_Matrix()’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor ‘beep::LA_Matrix::LA_Matrix()’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -DBOOST_MPI_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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /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-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc [ 81%] Linking CXX shared library libprime-phylo.so cd /build/prime-phylo-cDBuCy/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/x86_64-linux-gnu-g++ -fPIC -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat 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"CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o" "CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o" "CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o" "CMakeFiles/prime-phylo.dir/MatrixCache.cc.o" "CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o" "CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o" "CMakeFiles/prime-phylo.dir/SeqIO.cc.o" "CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o" "CMakeFiles/prime-phylo.dir/SequenceType.cc.o" "CMakeFiles/prime-phylo.dir/SequenceData.cc.o" "CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o" "CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o" "CMakeFiles/prime-phylo.dir/LA_Vector.cc.o" "CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o" "CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o" -L/usr/lib/x86_64-linux-gnu/liblapack.so -L/usr/lib/x86_64-linux-gnu/libblas.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu/liblapack.so:/usr/lib/x86_64-linux-gnu/libblas.so:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../sfile/libprime-phylo-sfile.so /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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[3]: Entering directory '/build/prime-phylo-cDBuCy/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/depend make[3]: Entering directory '/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake "--color=" primeDTLSR [ 82%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 82%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake "--color=" primeGEM cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:9: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:2: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:15: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:16: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:17: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:18: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:7: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function ‘int main(int, char**)’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:27: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:28: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/primeGEM.dir/link.d CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake "--color=" primeDLRS make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc [ 84%] Linking CXX executable primeDTLSR cd /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:9: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/algorithm:62, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:1: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:10: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh: At global scope: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:14: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:15: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:27: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:28: /build/prime-phylo-cDBuCy/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; | ^~~~~~~~ /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/primeDTLSR.dir/link.d CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 85%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake "--color=" treesize make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:8: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc: In function ‘int main(int, char**)’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/treesize.dir/link.d CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 87%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/showtree /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake "--color=" showtree make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:3: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:4: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function ‘int main(int, char**)’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/showtree.dir/link.d CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 91%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake "--color=" reconcile make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 92%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/primeDLRS.dir/link.d CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 make[3]: Leaving directory '/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 92%] Built target primeDLRS make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend make[3]: Entering directory '/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 93%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reroot /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake "--color=" reroot make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc:1: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:10: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:14: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ [ 93%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function ‘int main(int, char**)’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.c In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:14: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function ‘int main(int, char**)’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function ‘void populateGsMap(beep::Tree, beep::StrStrMap&)’: /build/prime-phylo-cDBuCy/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-cDBuCy/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/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/reroot.dir/link.d CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 95%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake "--color=" tree2leafnames make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.c In file included from /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:7: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:9: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: ‘virtual beep::Real beep::Tree::imbalance(beep::Node*)’ was hidden [-Woverloaded-virtual=] 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: ‘virtual beep::Real beep::Tree::imbalance()’ was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by ‘beep::Real beep::HybridTree::imbalance() const’ 94 | Real imbalance() const; | ^~~~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)’ was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by ‘beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)’ 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function ‘int main(int, char**)’: /build/prime-phylo-cDBuCy/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-cDBuCy/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) { | ^ [ 97%] Linking CXX executable reconcile cd /build/prime-phylo-cDBuCy/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 [ 98%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c [ 98%] Linking CXX executable tree2leafnames cd /build/prime-phylo-cDBuCy/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/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/reconcile.dir/link.d CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 98%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw cd /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake "--color=" chainsaw make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11=. -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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tree2leafnames.dir/link.d CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/x86_64-linux-gnu-gcc -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_GRAPH_DYN_LINK -DBOOST_GRAPH_NO_LIB -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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘beep::Tree ReadHostTree(gengetopt_args_info&)’: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘int main(int, char**)’: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/prime-phylo-cDBuCy/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chainsaw.dir/link.d CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libxml2.so /usr/lib/x86_64-linux-gnu/libboost_mpi.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.90.0 /usr/lib/x86_64-linux-gnu/libboost_graph.so.1.90.0 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.90.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [100%] Built target chainsaw make[2]: Leaving directory '/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-cDBuCy/prime-phylo-1.0.11 -B/build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/chainsaw.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDLRS.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/primeGEM.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reconcile.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/reroot.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/showtree.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1 -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/share/man/man1/treesize.1 -- Installing: /build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/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-cDBuCy/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-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw -- Set non-toolchain portion of runtime path of "/build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo" -- Installing: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11/debian/prime-phylo/usr/bin/mcmc_analysis make[1]: Leaving directory '/build/prime-phylo-cDBuCy/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-cDBuCy/prime-phylo-1.0.11' dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so make[1]: Leaving directory '/build/prime-phylo-cDBuCy/prime-phylo-1.0.11' dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: cannot extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: cannot extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: cannot extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: cannot extract name and version from library name 'libprime-phylo-sfile.so' dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-14_amd64.deb'. dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-14_amd64.deb'. dpkg-genbuildinfo -O../prime-phylo_1.0.11-14_amd64.buildinfo dpkg-genchanges -O../prime-phylo_1.0.11-14_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 2026-07-12T05:35:11Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 12 Jul 2026 05:35:12 +0000 | +------------------------------------------------------------------------------+ prime-phylo_1.0.11-14_amd64.changes: ------------------------------------ Format: 1.8 Date: Mon, 22 Sep 2025 21:44:48 +0200 Source: prime-phylo Binary: prime-phylo prime-phylo-dbgsym Architecture: source amd64 Version: 1.0.11-14 Distribution: perl-5.44-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: 1097647 1113421 Changes: prime-phylo (1.0.11-14) unstable; urgency=medium . * gcc-15.patch: new: fix build failures with gcc-15. (Closes: #1097647) * cmake-4.patch: new: fix build failure past cmake 4. (Closes: #1113421) * d/watch: convert to v5 untrackable upstream. * d/control: R³ now defaults to no, thus redundant. * d/patches/*: normalize Last-Update timestamp. * d/control: declare compliance to standards version 4.7.2. Checksums-Sha1: fd74f0ec7faddd256178e3e02a3008501f8d8d2d 1335 prime-phylo_1.0.11-14.dsc b24b459651979a69c2c09697e9221b79bcc9c0e9 11764 prime-phylo_1.0.11-14.debian.tar.xz 7b537515da664b9d6e4e5380d579ce00f3fcc667 10029988 prime-phylo-dbgsym_1.0.11-14_amd64.deb 421b516b7f3542f9ffbd028e9970bae2412c99ba 9680 prime-phylo_1.0.11-14_amd64.buildinfo f90455bf463ee5502076a43df170b5e545398340 836128 prime-phylo_1.0.11-14_amd64.deb Checksums-Sha256: 27f357f6e8f27b53b72b271974a7cd2803f8ceaa2953ad4968e10784a8c28155 1335 prime-phylo_1.0.11-14.dsc 310bef2d7da74326c5ca66e22f4515f42f815cf4b410f6f172ead3848d165b7c 11764 prime-phylo_1.0.11-14.debian.tar.xz f4be2b37cfa026e454d2cc3915d0053f3731639b6c0ae77e9048ed387271ea0c 10029988 prime-phylo-dbgsym_1.0.11-14_amd64.deb 23add43018be1bce86d9307528fde8fe3cd76e6f36df863a858b545dd191079f 9680 prime-phylo_1.0.11-14_amd64.buildinfo bfbb39abe8552a50c981bafed678ca5ab2861da6a2c1927a5dd20209d454dfbd 836128 prime-phylo_1.0.11-14_amd64.deb Files: 923350feb785389f1f10343b5d50e155 1335 science optional prime-phylo_1.0.11-14.dsc aa3d8040380428ba77bfd68fd2c255b8 11764 science optional prime-phylo_1.0.11-14.debian.tar.xz 791ab693a75af0b2de9219488a052c48 10029988 debug optional prime-phylo-dbgsym_1.0.11-14_amd64.deb 3a140946ec53dc0265332bb0c4ed3bb1 9680 science optional prime-phylo_1.0.11-14_amd64.buildinfo 3c459769e539d6a6ed372b3b3d4da49a 836128 science optional prime-phylo_1.0.11-14_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 12 Jul 2026 05:35:12 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: prime-phylo Binary: prime-phylo prime-phylo-dbgsym Architecture: amd64 source Version: 1.0.11-14 Checksums-Md5: 923350feb785389f1f10343b5d50e155 1335 prime-phylo_1.0.11-14.dsc 791ab693a75af0b2de9219488a052c48 10029988 prime-phylo-dbgsym_1.0.11-14_amd64.deb 3c459769e539d6a6ed372b3b3d4da49a 836128 prime-phylo_1.0.11-14_amd64.deb Checksums-Sha1: fd74f0ec7faddd256178e3e02a3008501f8d8d2d 1335 prime-phylo_1.0.11-14.dsc 7b537515da664b9d6e4e5380d579ce00f3fcc667 10029988 prime-phylo-dbgsym_1.0.11-14_amd64.deb f90455bf463ee5502076a43df170b5e545398340 836128 prime-phylo_1.0.11-14_amd64.deb Checksums-Sha256: 27f357f6e8f27b53b72b271974a7cd2803f8ceaa2953ad4968e10784a8c28155 1335 prime-phylo_1.0.11-14.dsc f4be2b37cfa026e454d2cc3915d0053f3731639b6c0ae77e9048ed387271ea0c 10029988 prime-phylo-dbgsym_1.0.11-14_amd64.deb bfbb39abe8552a50c981bafed678ca5ab2861da6a2c1927a5dd20209d454dfbd 836128 prime-phylo_1.0.11-14_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 12 Jul 2026 05:35:11 +0000 Build-Path: /build/prime-phylo-cDBuCy/prime-phylo-1.0.11 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bison (= 2:3.8.2+dfsg-1+b3), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), cmake (= 4.3.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), flex (= 2.6.4-8.2+b5), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gengetopt (= 2.23+dfsg1-1), gettext (= 1.0-3), gettext-base (= 1.0-3), gfortran (= 4:15.2.0-5+b1), gfortran-15 (= 15.3.0-1), gfortran-15-x86-64-linux-gnu (= 15.3.0-1), gfortran-x86-64-linux-gnu (= 4:15.2.0-5+b1), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), ibverbs-providers (= 63.0-2), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.4.0-1), libamd-comgr3 (= 7.0.2+dfsg-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.8.8-2), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblas-dev (= 3.12.1-8), libblas3 (= 3.12.1-8), libblkid1 (= 2.42.2-1), libboost-container1.90-dev (= 1.90.0-6), libboost-container1.90.0 (= 1.90.0-6), libboost-dev (= 1.90.0.2), libboost-exception1.90-dev (= 1.90.0-6), libboost-graph1.90-dev (= 1.90.0-6), libboost-graph1.90.0 (= 1.90.0-6), libboost-mpi-dev (= 1.90.0.2), libboost-mpi1.90-dev (= 1.90.0-6), libboost-mpi1.90.0 (= 1.90.0-6), libboost-regex1.90-dev (= 1.90.0-6), libboost-regex1.90.0 (= 1.90.0-6), libboost-serialization-dev (= 1.90.0.2), libboost-serialization1.90-dev (= 1.90.0-6), libboost-serialization1.90.0 (= 1.90.0-6), libboost-test1.90-dev (= 1.90.0-6), libboost-test1.90.0 (= 1.90.0-6), libboost1.90-dev (= 1.90.0-6), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-3), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcbor0.10 (= 0.10.2-2.1+b1), libcc1-0 (= 16.1.0-2), libclang-common-21-dev (= 1:21.1.8-7+b4), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl4t64 (= 8.21.0-2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.134-3), libdrm-common (= 2.4.134-3), libdrm2 (= 2.4.134-3), libedit2 (= 3.1-20260512-1), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libevent-core-2.1-7t64 (= 2.1.13-stable-1), libevent-dev (= 2.1.13-stable-1), libevent-extra-2.1-7t64 (= 2.1.13-stable-1), libevent-openssl-2.1-7t64 (= 2.1.13-stable-1), libevent-pthreads-2.1-7t64 (= 2.1.13-stable-1), libexpat1 (= 2.8.2-1), libfabric1 (= 2.1.0-1.1+b2), libffi8 (= 3.5.2-4), libfido2-1 (= 1.17.0-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libfuse3-4 (= 3.18.2-2), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran-15-dev (= 15.3.0-1), libgfortran5 (= 16.1.0-2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhwasan0 (= 16.1.0-2), libhwloc-dev (= 2.14.0-2), libhwloc-plugins (= 2.14.0-2), libhwloc15 (= 2.14.0-2), libibmad5 (= 63.0-2), libibumad3 (= 63.0-2), libibverbs-dev (= 63.0-2), libibverbs1 (= 63.0-2), libidn2-0 (= 2.3.8-5), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp26 (= 1.9.8-1), libk5crypto3 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), liblapack-dev (= 3.12.1-8), liblapack3 (= 3.12.1-8), libldap2 (= 2.6.13+dfsg-1+b1), libllvm21 (= 1:21.1.8-7+b4), liblsan0 (= 16.1.0-2), libltdl-dev (= 2.5.4-11), libltdl7 (= 2.5.4-11), liblz4-1 (= 1.10.0-10), liblzma-dev (= 5.8.3-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncursesw6 (= 6.6+20260608-2), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-ossl0 (= 1.22.1-1), libnl-3-200 (= 3.12.0-2+b1), libnl-3-dev (= 3.12.0-2+b1), libnl-route-3-200 (= 3.12.0-2+b1), libnl-route-3-dev (= 3.12.0-2+b1), libnuma-dev (= 2.0.19-1+b2), libnuma1 (= 2.0.19-1+b2), libopenmpi-dev (= 5.0.10-1), libopenmpi40 (= 5.0.10-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpciaccess0 (= 0.19-2), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libpmix2t64 (= 6.0.0+really5.0.9-3+b2), libproc2-1 (= 2:4.0.6-2), libprrte-bin (= 3.0.13-3), libprrte-dev (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsl5t64 (= 0.22.0-1), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 16.1.0-2), librdmacm1t64 (= 63.0-2), librhash1 (= 1.4.6-1.1+b1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1), libselinux1 (= 3.11-2), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libssh2-1t64 (= 1.11.1-4), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd-shared (= 261.1-2), libsystemd0 (= 261.1-2), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libtss2-esys-3.0.2-0t64 (= 4.1.3-6), libtss2-mu-4.0.1-0t64 (= 4.1.3-6), libtss2-rc0t64 (= 4.1.3-6), libtss2-sys1t64 (= 4.1.3-6), libtss2-tcti-cmd0t64 (= 4.1.3-6), libtss2-tcti-device0t64 (= 4.1.3-6), libtss2-tcti-mssim0t64 (= 4.1.3-6), libtss2-tcti-swtpm0t64 (= 4.1.3-6), libubsan1 (= 16.1.0-2), libucc1 (= 1.8.0-2), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.22.0~rc1-1), libudev1 (= 261.1-2), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libuv1t64 (= 1.52.1-4), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.3+dfsg-1), libxml2-dev (= 2.15.3+dfsg-1), libxnvctrl0 (= 535.171.04-1+b3), libxxhash0 (= 0.8.3-2+b2), libz3-4 (= 4.13.3-1.1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mount (= 2.42.2-1), mpi-default-dev (= 1.20), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.4p1-1), openssh-common (= 1:10.4p1-1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), pci.ids (= 0.0~2026.07.06-1), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), po-debconf (= 1.0.22), procps (= 2:4.0.6-2), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), systemd (= 261.1-2), systemd-tpm (= 261.1-2), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), tpm-udev (= 4.1.3-6), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1758570288" +------------------------------------------------------------------------------+ | Package contents Sun, 12 Jul 2026 05:35:12 +0000 | +------------------------------------------------------------------------------+ prime-phylo-dbgsym_1.0.11-14_amd64.deb -------------------------------------- new Debian package, version 2.0. size 10029988 bytes: control archive=1096 bytes. 802 bytes, 12 lines control 1254 bytes, 12 lines md5sums Package: prime-phylo-dbgsym Source: prime-phylo Version: 1.0.11-14 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 10542 Depends: prime-phylo (= 1.0.11-14) Section: debug Priority: optional Description: debug symbols for prime-phylo Build-Ids: 1a478f7051de827ebd98aa541b597210470d388e 23c2733b499c994fd32eb697571aee1223179f68 35d057204975a7355a6dc6e1c9f1102fd9f0d26c 568304cb1110f0701e5cefadfb7e9be922775c92 6816d6af23f4c44d7dbc66b05850448ad8bea3ff 7eb5f8e80a49374f104a1e84aba37aac96f8754d afba64304c4f40fa62b852da3ec163736a397196 c9495ced1addaaa859b1014ddc6473f1b5cb49fd cd976bb5d08b6be927921d9bb2dc964b269cddff f6403599dd10cd400409bef0528a63a65666560c fc416abb84e78762ec2a283c342516623d3228fd drwxr-xr-x root/root 0 2025-09-22 19:44 ./ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/1a/ -rw-r--r-- root/root 42648 2025-09-22 19:44 ./usr/lib/debug/.build-id/1a/478f7051de827ebd98aa541b597210470d388e.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/23/ -rw-r--r-- root/root 79264 2025-09-22 19:44 ./usr/lib/debug/.build-id/23/c2733b499c994fd32eb697571aee1223179f68.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/35/ -rw-r--r-- root/root 311128 2025-09-22 19:44 ./usr/lib/debug/.build-id/35/d057204975a7355a6dc6e1c9f1102fd9f0d26c.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/56/ -rw-r--r-- root/root 62480 2025-09-22 19:44 ./usr/lib/debug/.build-id/56/8304cb1110f0701e5cefadfb7e9be922775c92.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/68/ -rw-r--r-- root/root 86768 2025-09-22 19:44 ./usr/lib/debug/.build-id/68/16d6af23f4c44d7dbc66b05850448ad8bea3ff.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/7e/ -rw-r--r-- root/root 9418336 2025-09-22 19:44 ./usr/lib/debug/.build-id/7e/b5f8e80a49374f104a1e84aba37aac96f8754d.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/af/ -rw-r--r-- root/root 157952 2025-09-22 19:44 ./usr/lib/debug/.build-id/af/ba64304c4f40fa62b852da3ec163736a397196.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/c9/ -rw-r--r-- root/root 127120 2025-09-22 19:44 ./usr/lib/debug/.build-id/c9/495ced1addaaa859b1014ddc6473f1b5cb49fd.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/cd/ -rw-r--r-- root/root 281752 2025-09-22 19:44 ./usr/lib/debug/.build-id/cd/976bb5d08b6be927921d9bb2dc964b269cddff.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/f6/ -rw-r--r-- root/root 43456 2025-09-22 19:44 ./usr/lib/debug/.build-id/f6/403599dd10cd400409bef0528a63a65666560c.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.build-id/fc/ -rw-r--r-- root/root 41192 2025-09-22 19:44 ./usr/lib/debug/.build-id/fc/416abb84e78762ec2a283c342516623d3228fd.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 113544 2025-09-22 19:44 ./usr/lib/debug/.dwz/x86_64-linux-gnu/prime-phylo.debug drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-22 19:44 ./usr/share/doc/prime-phylo-dbgsym -> prime-phylo prime-phylo_1.0.11-14_amd64.deb ------------------------------- new Debian package, version 2.0. size 836128 bytes: control archive=1828 bytes. 1093 bytes, 19 lines control 2172 bytes, 33 lines md5sums Package: prime-phylo Version: 1.0.11-14 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3115 Depends: perl:any, libblas3 | libblas.so.3, libboost-mpi1.90.0 (>= 1.90.0), libboost-serialization1.90.0 (>= 1.90.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), liblapack3 | liblapack.so.3, libopenmpi40 (>= 5.0.10), libstdc++6 (>= 14), libxml2-16 (>= 2.14.1) 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 2025-09-22 19:44 ./ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/bin/ -rwxr-xr-x root/root 39704 2025-09-22 19:44 ./usr/bin/chainsaw -rwxr-xr-x root/root 33128 2012-12-17 15:52 ./usr/bin/mcmc_analysis -rwxr-xr-x root/root 108960 2025-09-22 19:44 ./usr/bin/primeDLRS -rwxr-xr-x root/root 113056 2025-09-22 19:44 ./usr/bin/primeDTLSR -rwxr-xr-x root/root 44344 2025-09-22 19:44 ./usr/bin/primeGEM lrwxrwxrwx root/root 0 2025-09-22 19:44 ./usr/bin/primeGSRf -> primeDLRS -rwxr-xr-x root/root 43680 2025-09-22 19:44 ./usr/bin/reconcile -rwxr-xr-x root/root 56184 2025-09-22 19:44 ./usr/bin/reroot -rwxr-xr-x root/root 35888 2025-09-22 19:44 ./usr/bin/showtree -rwxr-xr-x root/root 23160 2025-09-22 19:44 ./usr/bin/tree2leafnames -rwxr-xr-x root/root 27296 2025-09-22 19:44 ./usr/bin/treesize drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/lib/prime-phylo/ -rw-r--r-- root/root 55376 2025-09-22 19:44 ./usr/lib/prime-phylo/libprime-phylo-sfile.so -rw-r--r-- root/root 2550136 2025-09-22 19:44 ./usr/lib/prime-phylo/libprime-phylo.so drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./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 2025-09-22 19:44 ./usr/share/doc/prime-phylo/README.test -rw-r--r-- root/root 740 2025-09-22 19:44 ./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 2025-09-22 19:44 ./usr/share/doc/prime-phylo/copyright drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/doc/prime-phylo/examples/ -rw-r--r-- root/root 393 2025-09-22 19:44 ./usr/share/doc/prime-phylo/examples/gse -rw-r--r-- root/root 162 2025-09-22 19:44 ./usr/share/doc/prime-phylo/examples/hostfile -rw-r--r-- root/root 3513 2025-09-22 19:44 ./usr/share/doc/prime-phylo/examples/seqfile -rw-r--r-- root/root 14 2025-09-22 19:44 ./usr/share/doc/prime-phylo/examples/treefile -rw-r--r-- root/root 974 2025-09-22 19:44 ./usr/share/doc/prime-phylo/run-unit-test drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 699 2025-09-22 19:44 ./usr/share/lintian/overrides/prime-phylo drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-22 19:44 ./usr/share/man/man1/ -rw-r--r-- root/root 653 2025-09-22 19:44 ./usr/share/man/man1/chainsaw.1.gz -rw-r--r-- root/root 1284 2025-09-22 19:44 ./usr/share/man/man1/mcmc_analysis.1.gz -rw-r--r-- root/root 2154 2025-09-22 19:44 ./usr/share/man/man1/primeDLRS.1.gz -rw-r--r-- root/root 1992 2025-09-22 19:44 ./usr/share/man/man1/primeDTLSR.1.gz -rw-r--r-- root/root 987 2025-09-22 19:44 ./usr/share/man/man1/primeGEM.1.gz lrwxrwxrwx root/root 0 2025-09-22 19:44 ./usr/share/man/man1/primeGSRf.1.gz -> primeDLRS.1.gz -rw-r--r-- root/root 654 2025-09-22 19:44 ./usr/share/man/man1/reconcile.1.gz -rw-r--r-- root/root 886 2025-09-22 19:44 ./usr/share/man/man1/reroot.1.gz -rw-r--r-- root/root 904 2025-09-22 19:44 ./usr/share/man/man1/showtree.1.gz -rw-r--r-- root/root 494 2025-09-22 19:44 ./usr/share/man/man1/tree2leafnames.1.gz -rw-r--r-- root/root 608 2025-09-22 19:44 ./usr/share/man/man1/treesize.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 12 Jul 2026 05:35:12 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 12 Jul 2026 05:35:12 +0000 | +------------------------------------------------------------------------------+ Purging /build/prime-phylo-cDBuCy Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 12 Jul 2026 05:35:14 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 164652 Build-Time: 221 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 16 Job: /srv/debomatic/incoming/prime-phylo_1.0.11-14.dsc Machine Architecture: amd64 Package: prime-phylo Package-Time: 241 Source-Version: 1.0.11-14 Space: 164652 Status: successful Version: 1.0.11-14 -------------------------------------------------------------------------------- Finished at 2026-07-12T05:35:11Z Build needed 00:04:01, 164652k disk space