https://launchpad.net/~liushuyu-011/+archive/ubuntu/misc/+build/28050319 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-041 5.4.0-176-generic #196-Ubuntu SMP Fri Mar 22 16:46:20 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 11 Apr 22:16:02 ntpdate[1843]: adjust time server 10.211.37.1 offset -0.002865 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-28050319 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0 Creating target for build PACKAGEBUILD-28050319 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-28050319 Starting target for build PACKAGEBUILD-28050319 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-28050319 'deb http://ppa.launchpadcontent.net/liushuyu-011/misc/ubuntu noble main' 'deb http://ftpmaster.internal/ubuntu noble main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-28050319 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-28050319 Adding trusted keys to build-PACKAGEBUILD-28050319 pub rsa4096/327405FE663500EF 2023-01-19 [SC] Key fingerprint = 0F73 C580 C3F1 33BB 71BC DBF4 3274 05FE 6635 00EF uid Launchpad PPA for Liu Shuyu RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-28050319 Updating target for build PACKAGEBUILD-28050319 Get:1 http://ppa.launchpadcontent.net/liushuyu-011/misc/ubuntu noble InRelease [17.8 kB] Get:2 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:3 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:4 http://ppa.launchpadcontent.net/liushuyu-011/misc/ubuntu noble/main armhf Packages [13.8 kB] Get:5 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:7 http://ppa.launchpadcontent.net/liushuyu-011/misc/ubuntu noble/main Translation-en [7504 B] Get:8 http://ftpmaster.internal/ubuntu noble/main armhf Packages [1325 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main Translation-en [511 kB] Get:10 http://ftpmaster.internal/ubuntu noble/restricted armhf Packages [4844 B] Get:11 http://ftpmaster.internal/ubuntu noble/restricted Translation-en [15.0 kB] Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.4 MB] Get:13 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6068 kB] Get:14 http://ftpmaster.internal/ubuntu noble/multiverse armhf Packages [172 kB] Get:15 http://ftpmaster.internal/ubuntu noble/multiverse Translation-en [115 kB] Get:16 http://ftpmaster.internal/ubuntu noble-updates/universe armhf Packages [2880 B] Get:17 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [948 B] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [330 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [144 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1368 B] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/restricted Translation-en [16.0 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [651 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [279 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [1320 B] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Translation-en [1812 B] Fetched 24.6 MB in 11s (2154 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libperl5.36* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf gcc-14-base gcc-arm-linux-gnueabihf libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 170 upgraded, 23 newly installed, 15 to remove and 0 not upgraded. Need to get 98.8 MB of archives. After this operation, 24.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libnsl-dev armhf 1.3.0-3build3 [66.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libc6-dev armhf 2.39-0ubuntu8 [1352 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libc-dev-bin armhf 2.39-0ubuntu8 [19.1 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-dev armhf 1.3.4+ds-1.1build1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf libnss-nisplus armhf 1.3-5build1 [20.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libnsl2 armhf 1.3.0-3build3 [36.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libgssapi-krb5-2 armhf 1.20.1-6ubuntu2 [119 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5-3 armhf 1.20.1-6ubuntu2 [321 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libk5crypto3 armhf 1.20.1-6ubuntu2 [78.6 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5support0 armhf 1.20.1-6ubuntu2 [31.4 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libacl1 armhf 2.3.2-1build1 [15.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu3 [45.1 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main armhf libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:17 http://ftpmaster.internal/ubuntu noble/main armhf libcap-ng0 armhf 0.8.4-2build2 [13.6 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libaudit1 armhf 1:3.1.2-2.1build1 [44.4 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu6 [160 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap2 armhf 1:2.66-5ubuntu2 [25.8 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcrypt1 armhf 1:4.4.36-4build1 [92.6 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpg-error-l10n all 1.47-3build2 [8064 B] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpg-error0 armhf 1.47-3build2 [61.6 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcrypt20 armhf 1.10.3-2build1 [454 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main armhf liblzma5 armhf 5.6.1+really5.4.5-1 [111 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libzstd1 armhf 1.5.5+dfsg2-2build1 [265 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu6 [45.0 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblz4-1 armhf 1.9.4-1build1 [58.0 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpcre2-8-0 armhf 10.42-4ubuntu2 [198 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main armhf libselinux1 armhf 3.5-2ubuntu2 [70.9 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu6 [171 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main armhf perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6build1 [661 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm6t64 armhf 1.23-5.1build1 [30.3 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm-compat4t64 armhf 1.23-5.1build1 [6216 B] Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libperl5.38t64 armhf 5.38.2-3.2build2 [4109 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main armhf perl armhf 5.38.2-3.2build2 [231 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main armhf perl-base armhf 5.38.2-3.2build2 [1671 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu5 [15.1 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libtext-iconv-perl armhf 1.7-8build3 [12.7 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main armhf libtext-charwidth-perl armhf 0.04-11build3 [8992 B] Get:42 http://ftpmaster.internal/ubuntu noble/main armhf libc6 armhf 2.39-0ubuntu8 [2828 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main armhf libc-bin armhf 2.39-0ubuntu8 [530 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main armhf openssl armhf 3.0.13-0ubuntu3 [974 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd-shared armhf 255.4-1ubuntu7 [2010 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu4 [238 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main armhf libssl3t64 armhf 3.0.13-0ubuntu3 [1558 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main armhf systemd-dev all 255.4-1ubuntu7 [104 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main armhf systemd-sysv armhf 255.4-1ubuntu7 [11.9 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main armhf systemd armhf 255.4-1ubuntu7 [3502 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd0 armhf 255.4-1ubuntu7 [411 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu4 [47.1 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules armhf 1.5.3-5ubuntu4 [260 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main armhf libapt-pkg6.0t64 armhf 2.7.14build2 [986 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main armhf libnettle8t64 armhf 3.9.1-2.2build1 [187 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main armhf libhogweed6t64 armhf 3.9.1-2.2build1 [187 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libp11-kit0 armhf 0.25.3-4ubuntu2 [258 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libunistring5 armhf 1.1-2build1 [513 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu3 [947 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main armhf apt armhf 2.7.14build2 [1368 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main armhf apt-utils armhf 2.7.14build2 [210 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bzip2 armhf 1.0.8-5.1 [33.5 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbz2-1.0 armhf 1.0.8-5.1 [31.1 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu2 [49.2 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main armhf debconf-i18n all 1.5.86 [205 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main armhf debconf all 1.5.86 [124 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main armhf libpam0g armhf 1.5.3-5ubuntu4 [62.0 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main armhf libseccomp2 armhf 2.5.5-1ubuntu3 [49.5 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libargon2-1 armhf 0~20190702+dfsg-4build1 [22.6 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main armhf libudev1 armhf 255.4-1ubuntu7 [166 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu3 [135 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjson-c5 armhf 0.17-1build1 [31.3 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu6 [34.7 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu6 [196 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu6 [133 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu4 [21.9 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkeyutils1 armhf 1.6.3-3build1 [8236 B] Get:78 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1build1 [73.3 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main armhf linux-libc-dev armhf 6.8.0-22.22 [1555 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main armhf gcc-14-base armhf 14-20240330-1ubuntu2 [47.4 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-s1 armhf 14-20240330-1ubuntu2 [41.5 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main armhf base-files armhf 13ubuntu9 [73.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.17build1 [89.0 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main armhf bash armhf 5.2.21-2ubuntu4 [668 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu6 [102 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main armhf coreutils armhf 9.4-3ubuntu6 [1280 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++6 armhf 14-20240330-1ubuntu2 [714 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxxhash0 armhf 0.8.2-2build1 [31.5 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgmp10 armhf 2:6.3.0+dfsg-2ubuntu5 [210 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libffi8 armhf 3.4.6-1build1 [21.2 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libidn2-0 armhf 2.3.7-2build1 [96.2 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtasn1-6 armhf 4.19.0-3build1 [37.2 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main armhf libdebconfclient0 armhf 0.271ubuntu3 [10.9 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf base-passwd armhf 3.6.3build1 [50.9 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libassuan0 armhf 2.5.6-1build1 [31.3 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu2 [590 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main armhf gpg armhf 2.4.4-2ubuntu17 [524 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main armhf gpg-agent armhf 2.4.4-2ubuntu17 [235 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main armhf gpgconf armhf 2.4.4-2ubuntu17 [115 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main armhf readline-common all 8.2-4build1 [56.5 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncursesw6 armhf 6.4+20240113-1ubuntu2 [119 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtinfo6 armhf 6.4+20240113-1ubuntu2 [90.8 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main armhf libreadline8t64 armhf 8.2-4build1 [129 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main armhf pinentry-curses armhf 1.2.1-3ubuntu5 [36.7 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main armhf init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main armhf libnpth0t64 armhf 1.6-3.1build1 [6998 B] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf gpgv armhf 2.4.4-2ubuntu17 [224 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tar armhf 1.35+dfsg-3build1 [236 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main armhf dpkg armhf 1.22.6ubuntu6 [1230 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main armhf dash armhf 0.5.12-6ubuntu5 [80.8 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main armhf diffutils armhf 1:3.10-1build1 [167 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf findutils armhf 4.9.0-5build1 [293 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf grep armhf 3.11-4build1 [157 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gzip armhf 1.12-1ubuntu3 [95.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf hostname armhf 3.23+nmu2ubuntu2 [10.4 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf login armhf 1:4.13+dfsg1-4ubuntu3 [200 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-bin armhf 6.4+20240113-1ubuntu2 [178 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sed armhf 4.9-2build1 [190 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu6 [1216 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sysvinit-utils armhf 3.08-6ubuntu3 [33.8 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu4 [22.0 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu4 [202 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu4 [571 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main armhf optipng armhf 0.7.8+ds-1build2 [109 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main armhf libpng16-16t64 armhf 1.6.43-5build1 [166 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main armhf init armhf 1.66ubuntu1 [6186 B] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu6 [117 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu6 [41.8 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libattr1 armhf 1:2.5.2-1build1 [10.2 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmd0 armhf 1.1.0-2build1 [23.0 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main armhf libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage-common all 3.5-1build5 [10.1 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsepol2 armhf 3.5-2build1 [263 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage2 armhf 3.5-1build5 [84.5 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf passwd armhf 1:4.13+dfsg1-4ubuntu3 [817 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main armhf libproc2-0 armhf 2:4.0.4-4ubuntu3 [49.0 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu4 [14.7 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mawk armhf 1.3.4.20240123-1build1 [115 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main armhf procps armhf 2:4.0.4-4ubuntu3 [700 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main armhf sensible-utils all 0.0.22 [22.5 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main armhf ca-certificates all 20240203 [159 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main armhf krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tzdata all 2024a-2ubuntu1 [273 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu6 [78.7 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main armhf libgpm2 armhf 1.20.7-11 [13.6 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libip4tc2 armhf 1.8.10-3ubuntu2 [21.3 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main armhf libjansson4 armhf 2.14-2build2 [28.2 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main armhf psmisc armhf 23.7-1build1 [176 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main armhf xz-utils armhf 5.6.1+really5.4.5-1 [267 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main armhf advancecomp armhf 2.5-1build1 [198 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main armhf libctf0 armhf 2.42-4ubuntu2 [87.7 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main armhf libctf-nobfd0 armhf 2.42-4ubuntu2 [88.0 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu2 [2925 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main armhf libbinutils armhf 2.42-4ubuntu2 [460 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main armhf binutils armhf 2.42-4ubuntu2 [3072 B] Get:159 http://ftpmaster.internal/ubuntu noble/main armhf binutils-common armhf 2.42-4ubuntu2 [217 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main armhf libsframe1 armhf 2.42-4ubuntu2 [13.1 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main armhf libubsan1 armhf 14-20240330-1ubuntu2 [1153 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 14-20240330-1ubuntu2 [125 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main armhf libatomic1 armhf 14-20240330-1ubuntu2 [7846 B] Get:164 http://ftpmaster.internal/ubuntu noble/main armhf libasan8 armhf 14-20240330-1ubuntu2 [2940 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main armhf g++-13 armhf 13.2.0-23ubuntu3 [14.5 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13 armhf 13.2.0-23ubuntu3 [450 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++-13-dev armhf 13.2.0-23ubuntu3 [2455 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-13-dev armhf 13.2.0-23ubuntu3 [899 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main armhf libcc1-0 armhf 14-20240330-1ubuntu2 [39.1 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13 armhf 13.2.0-23ubuntu3 [1034 B] Get:171 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-base armhf 13.2.0-23ubuntu3 [48.6 kB] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libisl23 armhf 0.26-3build1 [544 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmpfr6 armhf 4.2.1-1build1 [229 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmpc3 armhf 1.3.1-1build1 [46.7 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [16.8 MB] Get:176 http://ftpmaster.internal/ubuntu noble/main armhf g++-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [9939 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [8759 kB] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++ armhf 4:13.2.0-7ubuntu2 [1084 B] Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc armhf 4:13.2.0-7ubuntu2 [5018 B] Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp armhf 4:13.2.0-7ubuntu2 [22.4 kB] Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu2 [5410 B] Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu2 [1214 B] Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu2 [964 B] Get:184 http://ftpmaster.internal/ubuntu noble/main armhf dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:185 http://ftpmaster.internal/ubuntu noble/main armhf libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf patch armhf 2.7.6-7build3 [110 kB] Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main armhf make armhf 4.3-4.1build2 [162 kB] Get:188 http://ftpmaster.internal/ubuntu noble/main armhf lto-disabled-list all 47 [12.4 kB] Get:189 http://ftpmaster.internal/ubuntu noble/main armhf libfakeroot armhf 1.33-1 [28.7 kB] Get:190 http://ftpmaster.internal/ubuntu noble/main armhf fakeroot armhf 1.33-1 [68.6 kB] Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblockfile-bin armhf 1.17-1build3 [10.5 kB] Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblockfile1 armhf 1.17-1build3 [6208 B] Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main armhf lockfile-progs armhf 0.1.19build2 [8062 B] Preconfiguring packages ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1build1) ... Preparing to unpack .../5-linux-libc-dev_6.8.0-22.22_armhf.deb ... Unpacking linux-libc-dev:armhf (6.8.0-22.22) over (6.5.0-9.9) ... Selecting previously unselected package gcc-14-base:armhf. Preparing to unpack .../6-gcc-14-base_14-20240330-1ubuntu2_armhf.deb ... Unpacking gcc-14-base:armhf (14-20240330-1ubuntu2) ... Setting up gcc-14-base:armhf (14-20240330-1ubuntu2) ... (Reading database ... 14977 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14-20240330-1ubuntu2_armhf.deb ... Unpacking libgcc-s1:armhf (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Setting up libgcc-s1:armhf (14-20240330-1ubuntu2) ... 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Setting up bash (5.2.21-2ubuntu4) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 14985 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu6_armhf.deb ... Unpacking bsdutils (1:2.39.3-9ubuntu6) over (1:2.39.1-4ubuntu2) ... Setting up bsdutils (1:2.39.3-9ubuntu6) ... (Reading database ... 14985 files and directories currently installed.) Removing usrmerge (35ubuntu1) ... (Reading database ... 14959 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3ubuntu6_armhf.deb ... Unpacking coreutils (9.4-3ubuntu6) over (9.1-1ubuntu2) ... Setting up coreutils (9.4-3ubuntu6) ... (Reading database ... 14964 files and directories currently installed.) Preparing to unpack .../libstdc++6_14-20240330-1ubuntu2_armhf.deb ... Unpacking libstdc++6:armhf (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4build1) ... Preparing to unpack .../pinentry-curses_1.2.1-3ubuntu5_armhf.deb ... Unpacking pinentry-curses (1.2.1-3ubuntu5) over (1.2.1-1ubuntu1) ... Preparing to unpack .../init-system-helpers_1.66ubuntu1_all.deb ... Unpacking init-system-helpers (1.66ubuntu1) over (1.65.2ubuntu1) ... Setting up init-system-helpers (1.66ubuntu1) ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu4) ... Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu4) ... Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu4) ... (Reading database ... 14977 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu4_armhf.deb ... 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Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:armhf (1:4.4.36-4build1) ... Setting up libasan8:armhf (14-20240330-1ubuntu2) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1build1) ... Setting up libkrb5-3:armhf (1.20.1-6ubuntu2) ... Setting up liblockfile1:armhf (1.17-1build3) ... Setting up libperl5.38t64:armhf (5.38.2-3.2build2) ... Setting up libbinutils:armhf (2.42-4ubuntu2) ... Setting up libisl23:armhf (0.26-3build1) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build2) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:armhf (14-20240330-1ubuntu2) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up libctf0:armhf (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up apt-utils (2.7.14build2) ... Setting up cpp-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build2) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19build2) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:armhf (8.2-4build1) ... Setting up libgcc-13-dev:armhf (13.2.0-23ubuntu3) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:armhf (2.39-0ubuntu8) ... Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu2) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu2) ... Setting up libstdc++-13-dev:armhf (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.1build1) ... Setting up binutils (2.42-4ubuntu2) ... Setting up gcc-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:armhf (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu2) ... Setting up libnsl2:armhf (1.3.0-3build3) ... Setting up gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu2) ... Setting up g++-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu2) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up libnss-nisplus:armhf (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu2) ... Setting up g++ (4:13.2.0-7ubuntu2) ... Setting up libnsl-dev:armhf (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15019 files and directories currently installed.) Purging configuration files for libssl3:armhf (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28050319 armhf noble -c chroot:build-PACKAGEBUILD-28050319 --arch=armhf --dist=noble --nolog prime-phylo_1.0.11-10ubuntu1.dsc Initiating build PACKAGEBUILD-28050319 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-176-generic #196-Ubuntu SMP Fri Mar 22 16:46:20 UTC 2024 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-041.buildd +==============================================================================+ | prime-phylo 1.0.11-10ubuntu1 (armhf) Thu, 11 Apr 2024 22:18:36 +0000 | +==============================================================================+ Package: prime-phylo Version: 1.0.11-10ubuntu1 Source Version: 1.0.11-10ubuntu1 Distribution: noble Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28050319/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/prime-phylo-D9Sdrn/resolver-2QbZcz' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- prime-phylo_1.0.11-10ubuntu1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/prime-phylo-D9Sdrn/prime-phylo-1.0.11' with '<>' I: NOTICE: Log filtering will replace 'build/prime-phylo-D9Sdrn' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ 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, fakeroot 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, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [447 B] Get:5 copy:/<>/apt_archive ./ Packages [530 B] Fetched 1934 B in 0s (30.9 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bison cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file flex gengetopt gettext gettext-base gfortran gfortran-13 gfortran-13-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf groff-base ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libbsd0 libcbor0.10 libcurl4t64 libdebhelper-perl libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu74 libjs-jquery libjs-jquery-ui libjsoncpp25 liblapack-dev liblapack3 libldap2 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpsl5t64 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-dev libxnvctrl0 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flex-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-13-doc libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost-graph1.83-dev libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk pkg-config m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: libfl-dev curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libssl3 libsasl2-modules xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bison cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file flex gengetopt gettext gettext-base gfortran gfortran-13 gfortran-13-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf groff-base ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libbsd0 libcbor0.10 libcurl4t64 libdebhelper-perl libdw1t64 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu74 libjs-jquery libjs-jquery-ui libjsoncpp25 liblapack-dev liblapack3 libldap2 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpsl5t64 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-dev libxnvctrl0 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 118 newly installed, 0 to remove and 0 not upgraded. Need to get 82.1 MB of archives. After this operation, 410 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnl-3-200 armhf 3.7.0-0.3build1 [49.0 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnl-route-3-200 armhf 3.7.0-0.3build1 [162 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main armhf libibverbs1 armhf 50.0-2build2 [57.9 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main armhf ibverbs-providers armhf 50.0-2build2 [27.4 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf icu-devtools armhf 74.2-1ubuntu3 [201 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblas-dev armhf 3.12.0-3build1 [132 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main armhf libboost1.83-dev armhf 1.83.0-2.1ubuntu3 [10.7 MB] Get:77 http://ftpmaster.internal/ubuntu noble/main armhf libboost-dev armhf 1.83.0.1ubuntu2 [4310 B] Get:78 http://ftpmaster.internal/ubuntu noble/main armhf libboost-serialization1.83.0 armhf 1.83.0-2.1ubuntu3 [332 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main armhf libboost-serialization1.83-dev armhf 1.83.0-2.1ubuntu3 [404 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main armhf libevent-core-2.1-7t64 armhf 2.1.12-stable-9ubuntu2 [82.6 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main armhf libevent-pthreads-2.1-7t64 armhf 2.1.12-stable-9ubuntu2 [7540 B] Get:82 http://ftpmaster.internal/ubuntu noble/main armhf librdmacm1t64 armhf 50.0-2build2 [63.0 kB] Get:83 http://ftpmaster.internal/ubuntu noble/universe armhf libfabric1 armhf 1.17.0-3build2 [419 kB] Get:84 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB] Get:85 http://ftpmaster.internal/ubuntu noble/universe armhf libmunge2 armhf 0.5.15-4build1 [17.1 kB] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpciaccess0 armhf 0.17-3build1 [16.3 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu4 [11.6 kB] Get:88 http://ftpmaster.internal/ubuntu noble/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1 [34.4 kB] Get:89 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-plugins armhf 2.10.0-1 [13.7 kB] Get:90 http://ftpmaster.internal/ubuntu noble/universe armhf libpmix2t64 armhf 5.0.1-4.1build1 [616 kB] Get:91 http://ftpmaster.internal/ubuntu noble/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu2 [2041 kB] Get:92 http://ftpmaster.internal/ubuntu noble/universe armhf libboost-mpi1.83.0 armhf 1.83.0-2.1ubuntu3 [268 kB] Get:93 http://ftpmaster.internal/ubuntu noble/universe armhf openmpi-common all 4.1.6-7ubuntu2 [170 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnl-3-dev armhf 3.7.0-0.3build1 [94.5 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnl-route-3-dev armhf 3.7.0-0.3build1 [196 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf libibverbs-dev armhf 50.0-2build2 [201 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnuma-dev armhf 2.0.18-1build1 [35.0 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libltdl7 armhf 2.4.7-7build1 [37.6 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libltdl-dev armhf 2.4.7-7build1 [166 kB] Get:100 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-dev armhf 2.10.0-1 [242 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-9ubuntu2 [127 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main armhf libevent-extra-2.1-7t64 armhf 2.1.12-stable-9ubuntu2 [56.1 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main armhf libevent-openssl-2.1-7t64 armhf 2.1.12-stable-9ubuntu2 [13.0 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main armhf libevent-dev armhf 2.1.12-stable-9ubuntu2 [264 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1ubuntu2 [880 kB] Get:106 http://ftpmaster.internal/ubuntu noble/universe armhf libpmix-dev armhf 5.0.1-4.1build1 [3936 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:108 http://ftpmaster.internal/ubuntu noble/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:109 http://ftpmaster.internal/ubuntu noble/universe armhf openmpi-bin armhf 4.1.6-7ubuntu2 [83.2 kB] Get:110 http://ftpmaster.internal/ubuntu noble/universe armhf libopenmpi-dev armhf 4.1.6-7ubuntu2 [816 kB] Get:111 http://ftpmaster.internal/ubuntu noble/universe armhf mpi-default-dev armhf 1.15 [3116 B] Get:112 http://ftpmaster.internal/ubuntu noble/universe armhf libboost-mpi1.83-dev armhf 1.83.0-2.1ubuntu3 [298 kB] Get:113 http://ftpmaster.internal/ubuntu noble/universe armhf libboost-mpi-dev armhf 1.83.0.1ubuntu2 [4144 B] Get:114 http://ftpmaster.internal/ubuntu noble/universe armhf libboost-serialization-dev armhf 1.83.0.1ubuntu2 [4280 B] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libicu-dev armhf 74.2-1ubuntu3 [11.6 MB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblapack-dev armhf 3.12.0-3build1 [2177 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main armhf libxml2-dev armhf 2.9.14+dfsg-1.3ubuntu3 [733 kB] Preconfiguring packages ... 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Setting up libpciaccess0:armhf (0.17-3build1) ... Setting up libxau6:armhf (1:1.0.9-1build6) ... Setting up libboost1.83-dev:armhf (1.83.0-2.1ubuntu3) ... Setting up gengetopt (2.23+dfsg1-1) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libcbor0.10:armhf (0.10.2-1.2ubuntu2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libbrotli1:armhf (1.1.0-2build2) ... Setting up libuv1t64:armhf (1.48.0-1.1build1) ... Setting up libmagic1t64:armhf (1:5.45-3build1) ... Setting up libpsl5t64:armhf (0.21.2-1.1build1) ... Setting up libnghttp2-14:armhf (1.59.0-1build2) ... Setting up gettext-base (0.21-14ubuntu2) ... Setting up m4 (1.4.19-4build1) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-9ubuntu2) ... Setting up file (1:5.45-3build1) ... Setting up libelf1t64:armhf (0.190-1.1build4) ... Setting up libdw1t64:armhf (0.190-1.1build4) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu3) ... Setting up libboost-serialization1.83.0:armhf (1.83.0-2.1ubuntu3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-3build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libmunge2:armhf (0.5.15-4build1) ... Setting up libx11-data (2:1.8.7-1build1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libhwloc15:armhf (2.10.0-1) ... Setting up autopoint (0.21-14ubuntu2) ... Setting up libjsoncpp25:armhf (1.9.5-6build1) ... Setting up libltdl7:armhf (2.4.7-7build1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu3) ... Setting up libssh-4:armhf (0.10.6-2build2) ... Setting up libgfortran5:armhf (14-20240330-1ubuntu2) ... Setting up autoconf (2.71-3) ... Setting up libicu74:armhf (74.2-1ubuntu3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu2) ... Setting up libnuma1:armhf (2.0.18-1build1) ... Setting up dwz (0.15-1build6) ... Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ... Setting up librhash0:armhf (1.4.3-3build1) ... Setting up libuchardet0:armhf (0.0.8-1build1) ... Setting up libnl-3-200:armhf (3.7.0-0.3build1) ... Setting up bison (2:3.8.2+dfsg-1build2) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up openmpi-common (4.1.6-7ubuntu2) ... Setting up debugedit (1:5.0-5build2) ... Setting up libsub-override-perl (0.10-1) ... Setting up cmake-data (3.28.3-1build6) ... Setting up libboost-dev:armhf (1.83.0.1ubuntu2) ... Setting up libevent-core-2.1-7t64:armhf (2.1.12-stable-9ubuntu2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:armhf (1.14.0-1build2) ... Setting up libgfortran-13-dev:armhf (13.2.0-23ubuntu3) ... Setting up libbsd0:armhf (0.12.1-1build1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu8) ... Setting up libblas-dev:armhf (3.12.0-3build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gfortran-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu6) ... Setting up flex (2.6.4-8.2build1) ... Setting up liblapack3:armhf (3.12.0-3build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-14ubuntu2) ... Setting up libcurl4t64:armhf (8.5.0-2ubuntu10) ... Setting up libtool (2.4.7-7build1) ... Setting up libevent-pthreads-2.1-7t64:armhf (2.1.12-stable-9ubuntu2) ... Setting up libedit2:armhf (3.1-20230828-1build1) ... Setting up libevent-openssl-2.1-7t64:armhf (2.1.12-stable-9ubuntu2) ... Setting up libboost-serialization1.83-dev:armhf (1.83.0-2.1ubuntu3) ... Setting up gfortran-arm-linux-gnueabihf (4:13.2.0-7ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:armhf (2.0.18-1build1) ... Setting up libnl-route-3-200:armhf (3.7.0-0.3build1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:armhf (2.4.7-7build1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up gfortran-13 (13.2.0-23ubuntu3) ... Setting up liblapack-dev:armhf (3.12.0-3build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up icu-devtools (74.2-1ubuntu3) ... Setting up libboost-serialization-dev:armhf (1.83.0.1ubuntu2) ... Setting up libevent-extra-2.1-7t64:armhf (2.1.12-stable-9ubuntu2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libnl-3-dev:armhf (3.7.0-0.3build1) ... Setting up groff-base (1.23.0-3build2) ... Setting up libx11-6:armhf (2:1.8.7-1build1) ... Setting up libhwloc-dev:armhf (2.10.0-1) ... Setting up libarchive13t64:armhf (3.7.2-2) ... Setting up libicu-dev:armhf (74.2-1ubuntu3) ... Setting up libibverbs1:armhf (50.0-2build2) ... Setting up ibverbs-providers:armhf (50.0-2build2) ... Setting up openssh-client (1:9.6p1-3ubuntu13) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (2:1.3.4-1build2) ... Setting up man-db (2.12.0-4build2) ... 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 (4:13.2.0-7ubuntu2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist Setting up libxnvctrl0:armhf (510.47.03-0ubuntu4) ... Setting up libnl-route-3-dev:armhf (3.7.0-0.3build1) ... Setting up libxml2-dev:armhf (2.9.14+dfsg-1.3ubuntu3) ... Setting up libevent-dev (2.1.12-stable-9ubuntu2) ... Setting up cmake (3.28.3-1build6) ... Setting up librdmacm1t64:armhf (50.0-2build2) ... Setting up libfabric1:armhf (1.17.0-3build2) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libibverbs-dev:armhf (50.0-2build2) ... Setting up libhwloc-plugins:armhf (2.10.0-1) ... Setting up libpmix2t64:armhf (5.0.1-4.1build1) ... Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu2) ... Setting up libboost-mpi1.83.0 (1.83.0-2.1ubuntu3) ... Setting up libpmix-dev:armhf (5.0.1-4.1build1) ... Setting up openmpi-bin (4.1.6-7ubuntu2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:armhf (4.1.6-7ubuntu2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up mpi-default-dev (1.15) ... Setting up libboost-mpi1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-mpi-dev (1.83.0.1ubuntu2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-176-generic #196-Ubuntu SMP Fri Mar 22 16:46:20 UTC 2024 arm64 (armv7l) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-22.22 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-arm-linux-gnueabihf_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 bison_2:3.8.2+dfsg-1build2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 cmake_3.28.3-1build6 cmake-data_3.28.3-1build6 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu2 cpp-13_13.2.0-23ubuntu3 cpp-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 cpp-arm-linux-gnueabihf_4:13.2.0-7ubuntu2 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5build1 flex_2.6.4-8.2build1 g++_4:13.2.0-7ubuntu2 g++-13_13.2.0-23ubuntu3 g++-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 g++-arm-linux-gnueabihf_4:13.2.0-7ubuntu2 gcc_4:13.2.0-7ubuntu2 gcc-13_13.2.0-23ubuntu3 gcc-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 gcc-13-base_13.2.0-23ubuntu3 gcc-14-base_14-20240330-1ubuntu2 gcc-arm-linux-gnueabihf_4:13.2.0-7ubuntu2 gengetopt_2.23+dfsg1-1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 gfortran_4:13.2.0-7ubuntu2 gfortran-13_13.2.0-23ubuntu3 gfortran-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 gfortran-arm-linux-gnueabihf_4:13.2.0-7ubuntu2 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-3build2 gzip_1.12-1ubuntu3 hostname_3.23+nmu2ubuntu2 ibverbs-providers_50.0-2build2 icu-devtools_74.2-1ubuntu3 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-1build1 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.7.14build2 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.2-2 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240330-1ubuntu2 libassuan0_2.5.6-1build1 libatomic1_14-20240330-1ubuntu2 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblas-dev_3.12.0-3build1 libblas3_3.12.0-3build1 libblkid1_2.39.3-9ubuntu6 libboost-dev_1.83.0.1ubuntu2 libboost-mpi-dev_1.83.0.1ubuntu2 libboost-mpi1.83-dev_1.83.0-2.1ubuntu3 libboost-mpi1.83.0_1.83.0-2.1ubuntu3 libboost-serialization-dev_1.83.0.1ubuntu2 libboost-serialization1.83-dev_1.83.0-2.1ubuntu3 libboost-serialization1.83.0_1.83.0-2.1ubuntu3 libboost1.83-dev_1.83.0-2.1ubuntu3 libbrotli1_1.1.0-2build2 libbsd0_0.12.1-1build1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8 libc-dev-bin_2.39-0ubuntu8 libc6_2.39-0ubuntu8 libc6-dev_2.39-0ubuntu8 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu2 libcbor0.10_0.10.2-1.2ubuntu2 libcc1-0_14-20240330-1ubuntu2 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcurl4t64_8.5.0-2ubuntu10 libdb5.3t64_5.3.28+dfsg2-6build1 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu6 libdw1t64_0.190-1.1build4 libedit2_3.1-20230828-1build1 libelf1t64_0.190-1.1build4 libevent-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-core-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-dev_2.1.12-stable-9ubuntu2 libevent-extra-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-openssl-2.1-7t64_2.1.12-stable-9ubuntu2 libevent-pthreads-2.1-7t64_2.1.12-stable-9ubuntu2 libexpat1_2.6.1-2build1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfabric1_1.17.0-3build2 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 libfido2-1_1.14.0-1build2 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-23ubuntu3 libgcc-s1_14-20240330-1ubuntu2 libgcrypt20_1.10.3-2build1 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgfortran-13-dev_13.2.0-23ubuntu3 libgfortran5_14-20240330-1ubuntu2 libgmp10_2:6.3.0+dfsg-2ubuntu5 libgnutls30t64_3.8.3-1.1ubuntu3 libgomp1_14-20240330-1ubuntu2 libgpg-error-l10n_1.47-3build2 libgpg-error0_1.47-3build2 libgpm2_1.20.7-11 libgssapi-krb5-2_1.20.1-6ubuntu2 libhogweed6t64_3.9.1-2.2build1 libhwloc-dev_2.10.0-1 libhwloc-plugins_2.10.0-1 libhwloc15_2.10.0-1 libibverbs-dev_50.0-2build2 libibverbs1_50.0-2build2 libicu-dev_74.2-1ubuntu3 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libip4tc2_1.8.10-3ubuntu2 libisl23_0.26-3build1 libjansson4_2.14-2build2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjson-c5_0.17-1build1 libjsoncpp25_1.9.5-6build1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu6 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 liblapack-dev_3.12.0-3build1 liblapack3_3.12.0-3build1 libldap2_2.6.7+dfsg-1~exp1ubuntu8 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 libltdl-dev_2.4.7-7build1 libltdl7_2.4.7-7build1 liblz4-1_1.9.4-1build1 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmd0_1.1.0-2build1 libmount1_2.39.3-9ubuntu6 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libmunge2_0.5.15-4build1 libncursesw6_6.4+20240113-1ubuntu2 libnettle8t64_3.9.1-2.2build1 libnghttp2-14_1.59.0-1build2 libnl-3-200_3.7.0-0.3build1 libnl-3-dev_3.7.0-0.3build1 libnl-route-3-200_3.7.0-0.3build1 libnl-route-3-dev_3.7.0-0.3build1 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-5build1 libnuma-dev_2.0.18-1build1 libnuma1_2.0.18-1build1 libopenmpi-dev_4.1.6-7ubuntu2 libopenmpi3t64_4.1.6-7ubuntu2 libp11-kit0_0.25.3-4ubuntu2 libpam-modules_1.5.3-5ubuntu4 libpam-modules-bin_1.5.3-5ubuntu4 libpam-runtime_1.5.3-5ubuntu4 libpam0g_1.5.3-5ubuntu4 libpciaccess0_0.17-3build1 libpcre2-8-0_10.42-4ubuntu2 libperl5.38t64_5.38.2-3.2build2 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libtirpc-dev_1.3.4+ds-1.1build1 libtirpc3t64_1.3.4+ds-1.1build1 libtool_2.4.7-7build1 libubsan1_14-20240330-1ubuntu2 libuchardet0_0.0.8-1build1 libudev1_255.4-1ubuntu7 libunistring2_1.0-2 libunistring5_1.1-2build1 libuuid1_2.39.3-9ubuntu6 libuv1t64_1.48.0-1.1build1 libx11-6_2:1.8.7-1build1 libx11-data_2:1.8.7-1build1 libxau6_1:1.0.9-1build6 libxcb1_1.15-1 libxdmcp6_1:1.1.3-0ubuntu6 libxext6_2:1.3.4-1build2 libxml2_2.9.14+dfsg-1.3ubuntu3 libxml2-dev_2.9.14+dfsg-1.3ubuntu3 libxnvctrl0_510.47.03-0ubuntu4 libxxhash0_0.8.2-2build1 libzstd1_1.5.5+dfsg2-2build1 linux-libc-dev_6.8.0-22.22 lockfile-progs_0.1.19build2 login_1:4.13+dfsg1-4ubuntu3 logsave_1.47.0-2.4~exp1ubuntu4 lto-disabled-list_47 m4_1.4.19-4build1 make_4.3-4.1build2 man-db_2.12.0-4build2 mawk_1.3.4.20240123-1build1 mount_2.39.3-9ubuntu6 mpi-default-dev_1.15 ncurses-base_6.4+20240113-1ubuntu2 ncurses-bin_6.4+20240113-1ubuntu2 ocl-icd-libopencl1_2.3.2-1 openmpi-bin_4.1.6-7ubuntu2 openmpi-common_4.1.6-7ubuntu2 openssh-client_1:9.6p1-3ubuntu13 openssl_3.0.13-0ubuntu3 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu3 patch_2.7.6-7build3 perl_5.38.2-3.2build2 perl-base_5.38.2-3.2build2 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3.2build2 pinentry-curses_1.2.1-3ubuntu5 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 systemd_255.4-1ubuntu7 systemd-dev_255.4-1ubuntu7 systemd-sysv_255.4-1ubuntu7 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 tzdata_2024a-2ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prime-phylo Binary: prime-phylo Architecture: any Version: 1.0.11-10ubuntu1 Maintainer: Ubuntu Developers Uploaders: Erik Sjolund , Andreas Tille Homepage: http://prime.sbc.su.se Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev Package-List: prime-phylo deb science optional arch=any Checksums-Sha1: 1dd3b086599e29f6a17319f8ebe294cd6eed0c07 750651 prime-phylo_1.0.11.orig.tar.gz e86270085ba62d56a5da8b63aa2284381c367ad0 9224 prime-phylo_1.0.11-10ubuntu1.debian.tar.xz Checksums-Sha256: 5d46b4e528417bb4a0be56756069f255f86ab58b28b55fa6a96983f10585bd8d 750651 prime-phylo_1.0.11.orig.tar.gz 10dd0091c8e53276bfa244b7b19365f3cabd7c74a571d8455942641053eda4fa 9224 prime-phylo_1.0.11-10ubuntu1.debian.tar.xz Files: 0356071434de01edf92a1b9182ed6ef1 750651 prime-phylo_1.0.11.orig.tar.gz a4a49c7c36041ede5c1017d8ee689766 9224 prime-phylo_1.0.11-10ubuntu1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEE6x/rcKrl3aOwzUVJI9HORTRBlDcFAmYYYNcACgkQI9HORTRB lDejQg/9HJtxLVR677G/T4gOk5P39DNr392LG/sbARyQk/k7v++t6e4J0CvdvJl7 g6p2JOHcjGYEbqFn2KbgOK1naeRc4ETNun4Qp6tfByOI/nS3v0pRGM2UlQXMUdDu 5TKRiXxsj9Pjqyi1XGhYm0osbXgFQJIKzyx2PDLnoq+1k8z+LfHoQa/oPCAWlXbp fwfHaD1b54BY6KWsXxvWl1gIL6lQ+zLp5VJfpUkXgvskKqv/kB/0nCLNy6UoxvnB doP1Bc/QWfyqKcmkG1NtXS6SivNdJLrMZ/Bkg5aESwkC4ukBZXfsEXI3t22B+f2z NnUuQd5trXkhWkVkudWTrU/HMGQzYDqLR7SpUlqoj4m6JdDwt90k4cw3MVqb0+qC k8BpsKYubO/6tDxWiQMw7eAijaeAkPGiWyfvE7rhesce7j6NTpDqmWUjVvEG0Xpr 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0004-fix-gcc10-build.patch dpkg-source: info: applying fix-ftbfs-with-gcc13.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28050319 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28050319 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28050319 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-10ubuntu1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary-arch dh binary-arch --buildsystem=cmake dh_update_autotools_config -a -O--buildsystem=cmake dh_autoreconf -a -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' 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-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 13.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- The Fortran compiler identification is GNU 13.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- The C compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so hittade /usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/liblapack.so;/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI_Fortran: /usr/lib/arm-linux-gnueabihf/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Found Boost: /usr/lib/arm-linux-gnueabihf/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.40.0") found components: mpi serialization -- Found LibXml2: /usr/lib/arm-linux-gnueabihf/libxml2.so (found version "2.9.14") mpilib is /usr/lib/arm-linux-gnueabihf/openmpi/include;/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi included path is CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDTLSR". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDTLSR/CMakeLists.txt:30 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDLRS". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDLRS/CMakeLists.txt:27 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "showtree". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/tools/showtree/CMakeLists.txt:12 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:120 (if): Policy CMP0053 is not set: Simplify variable reference and escape sequence evaluation. Run "cmake --help-policy CMP0053" for policy details. Use the cmake_policy command to set the policy and suppress this warning. For input: '@CMAKE_SOURCE_DIR@/excluded_from_release' the old evaluation rules produce: '/<>/excluded_from_release' but the new evaluation rules produce: '@CMAKE_SOURCE_DIR@/excluded_from_release' Using the old result for compatibility since the policy is not set. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (15.3s) 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: /<>/src/cxx/tools/tree2leafnames/tree2leafnames.cc This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (0.3s) 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: /<>/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>' dh_auto_build -a -O--buildsystem=cmake cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles /<>/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' 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 '/<>/obj-arm-linux-gnueabihf' [ 1%] [BISON][MyParser2] Building parser with bison 3.8.2 [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 cd /<>/src/cxx/libraries/sfile && /usr/bin/flex -o/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c seqreader.l cd /<>/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /<>/obj-arm-linux-gnueabihf/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 /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/libraries/sfile /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' 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 '/<>/obj-arm-linux-gnueabihf' [ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/sfile/gbread.c [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/sfile/sfile.c [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c /<>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’: /<>/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 /<>/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable ‘date’ set but not used [-Wunused-but-set-variable] 212 | char *top, *date; | ^~~~ gb.y: In function ‘add_to_seq’: gb.y:403:9: warning: unused variable ‘new_buf’ [-Wunused-variable] seqreader.l: In function ‘seq_read’: seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable] /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c: At top level: /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function] 1864 | static int input (void) | ^~~~~ /<>/obj-arm-linux-gnueabihf/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 ) | ^~~~~~~ /<>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_add_comment’: /<>/src/cxx/libraries/sfile/sfile.c:303:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[4]’ [-Warray-bounds=] 303 | tmp->text = strdup(s); | ^~ /<>/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 4 allocated by ‘malloc’ 301 | tmp = (struct comment *) malloc(sizeof(struct comment *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/sfile/sfile.c:304:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[4]’ [-Warray-bounds=] 304 | tmp->next = NULL; | ^~ /<>/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 4 allocated by ‘malloc’ 301 | tmp = (struct comment *) malloc(sizeof(struct comment *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 4%] Linking C shared library libprime-phylo-sfile.so cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so "CMakeFiles/prime-phylo-sfile.dir/gbread.c.o" "CMakeFiles/prime-phylo-sfile.dir/sfile.c.o" "CMakeFiles/prime-phylo-sfile.dir/lexer.c.o" "CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o" -Wl,-rpath,:::::::::::::::::::: make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 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 '/<>/obj-arm-linux-gnueabihf' [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 [ 5%] [BISON][MyParser] Building parser with bison 3.8.2 cd /<>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c NHX.l cd /<>/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /<>/obj-arm-linux-gnueabihf/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 /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/libraries/prime /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' 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 '/<>/obj-arm-linux-gnueabihf' [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/NHXnode.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/NHXtree.c cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/NHXannotation.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c /<>/src/cxx/libraries/prime/NHXnode.c: In function ‘NHX_debug_print’: /<>/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 [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c /<>/src/cxx/libraries/prime/NHXannotation.c: In function ‘new_annotation’: /<>/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); | ^ /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1597:16: warning: ‘input’ defined but not used [-Wunused-function] 1597 | static int input (void) | ^~~~~ /<>/obj-arm-linux-gnueabihf/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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/AnError.cc NHXparse.y: In function ‘read_tree’: NHXparse.y:354:11: warning: passing argument 1 of ‘close’ makes integer from pointer without a cast [-Wint-conversion] In file included from NHXparse.y:5: /usr/include/unistd.h:358:23: note: expected ‘int’ but argument is of type ‘FILE *’ 358 | extern int close (int __fd); | ~~~~^~~~ 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 *’ [ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Beep.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BeepOption.cc [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Hacks.cc [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ODESolver.cc /<>/src/cxx/libraries/prime/BeepOption.cc: In member function ‘std::pair beep::option::BeepOptionMap::getDoubleX2(std::string)’: /<>/src/cxx/libraries/prime/BeepOption.cc:592:59: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 592 | pair BeepOptionMap::getDoubleX2(string name) | ^ [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/PRNG.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -MF CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o.d -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /<>/src/cxx/libraries/prime/PrimeOptionMap.cc In file included from /<>/src/cxx/libraries/prime/ODESolver.cc:4: /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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 /<>/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /<>/src/cxx/libraries/prime/PrimeOption.hh: In member function ‘void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)’: /<>/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 405 | catch(std::exception e) | ^ /<>/src/cxx/libraries/prime/PrimeOption.hh:423:30: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 423 | catch(std::exception e) | ^ [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ProbabilityModel.cc [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/DiscreteGamma.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/BeepOption.hh:10, from /<>/src/cxx/libraries/prime/BeepOption.cc:5: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::option::BeepOptionMap::parseUserSubstModel(beep::option::UserSubstModelOption*, int&, int, char**)’ at /<>/src/cxx/libraries/prime/BeepOption.cc:360:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::option::BeepOptionMap::parseUserSubstModel(beep::option::UserSubstModelOption*, int&, int, char**)’ at /<>/src/cxx/libraries/prime/BeepOption.cc:375:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Probability.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/PrimeOptionMap.hh:12, from /<>/src/cxx/libraries/prime/PrimeOptionMap.cc:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::TmplPrimeOption::parseParams(std::string&, unsigned int, std::vector&) [with T = double]’ at /<>/src/cxx/libraries/prime/PrimeOption.hh:286:22: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)’ at /<>/src/cxx/libraries/prime/PrimeOption.hh:400:16: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)’ at /<>/src/cxx/libraries/prime/PrimeOption.hh:415:16: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)’ at /<>/src/cxx/libraries/prime/BeepOption.cc:624:13: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)’ at /<>/src/cxx/libraries/prime/BeepOption.cc:625:13: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)’ at /<>/src/cxx/libraries/prime/BeepOption.cc:626:13: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Tokenizer.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TimeEstimator.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BranchSwapping.cc [ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/DiscTree.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeDiscTree.cc In file included from /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6: /<>/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /<>/src/cxx/libraries/prime/AnError.hh:1, from /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:3: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EpochPtMaps.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/DiscTree.hh:6, from /<>/src/cxx/libraries/prime/DiscTree.cc:6: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::DiscTree::createGridTimes()’ at /<>/src/cxx/libraries/prime/DiscTree.cc:55:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EpochPtSet.cc [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EpochTree.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/EpochPtSet.hh:6, from /<>/src/cxx/libraries/prime/EpochPtSet.cc:5: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /<>/src/cxx/libraries/prime/EpochPtMaps.cc:5: /<>/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; | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘beep::EpochPtSet::EpochPtSet(std::vector, beep::Real, beep::Real, unsigned int)’ at /<>/src/cxx/libraries/prime/EpochPtSet.cc:22:19: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘beep::EpochPtSet::EpochPtSet(std::vector, beep::Real, beep::Real, unsigned int)’ at /<>/src/cxx/libraries/prime/EpochPtSet.cc:25:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘beep::EpochPtSet::EpochPtSet(std::vector, beep::Real, beep::Real, unsigned int)’ at /<>/src/cxx/libraries/prime/EpochPtSet.cc:27:19: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.hh:7, from /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:4: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 [ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/InvMRCA.cc In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {const vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >*, vector >, allocator > > > >; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21, inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::vector >*; _ForwardIterator = std::vector >*; bool _TrivialValueTypes = false]’ at /usr/include/c++/13/bits/stl_uninitialized.h:137:32, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = vector >*; _ForwardIterator = vector >*; _Tp = vector >]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::vector >; _Alloc = std::allocator > >]’ at /usr/include/c++/13/bits/vector.tcc:257:35: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘Type beep::BeepVector::operator[](unsigned int) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:148:21, inlined from ‘Type beep::BeepVector::operator[](const beep::Node&) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:117:44, inlined from ‘Type beep::BeepVector::operator[](const beep::Node*) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:129:33, inlined from ‘std::string beep::EdgeDiscPtMap::printPath(const beep::Node*) const [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:349:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘Type beep::BeepVector::operator[](unsigned int) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:148:21, inlined from ‘Type beep::BeepVector::operator[](const beep::Node&) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:117:44, inlined from ‘Type beep::BeepVector::operator[](const beep::Node*) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:129:33, inlined from ‘std::string beep::EdgeDiscPtMap::print() const [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:265:43: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘Type beep::BeepVector::operator[](unsigned int) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:148:21, inlined from ‘Type beep::BeepVector::operator[](const beep::Node&) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:117:44, inlined from ‘Type beep::BeepVector::operator[](const beep::Node*) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:129:33, inlined from ‘beep::EdgeDiscretizer::Point beep::EdgeDiscPtMap::getTopmostPt() const [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:95:39: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘Type beep::BeepVector::operator[](unsigned int) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:148:21, inlined from ‘Type beep::BeepVector::operator[](const beep::Node&) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:117:44, inlined from ‘Type beep::BeepVector::operator[](const beep::Node*) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:129:33, inlined from ‘const T& beep::EdgeDiscPtMap::operator()(const beep::Node*) const [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.hh:112:23: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘Type beep::BeepVector::operator[](unsigned int) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:148:21, inlined from ‘Type beep::BeepVector::operator[](const beep::Node&) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:117:44, inlined from ‘Type beep::BeepVector::operator[](const beep::Node*) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:129:33, inlined from ‘unsigned int beep::EdgeDiscPtMap::getNoOfPts(const beep::Node*) const [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.hh:130:28: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘Type beep::BeepVector::operator[](unsigned int) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:148:21, inlined from ‘Type beep::BeepVector::operator[](const beep::Node&) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:117:44, inlined from ‘Type beep::BeepVector::operator[](const beep::Node*) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:129:33, inlined from ‘const T& beep::EdgeDiscPtMap::operator()(const beep::EdgeDiscretizer::Point&) const [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.hh:92:27: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘Type beep::BeepVector::operator[](unsigned int) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:148:21, inlined from ‘Type beep::BeepVector::operator[](const beep::Node&) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:117:44, inlined from ‘Type beep::BeepVector::operator[](const beep::Node*) const [with Type = std::vector >]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:129:33, inlined from ‘const T& beep::EdgeDiscPtMap::getTopmost() const [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:87:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Node.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/EpochPtMaps.hh:7: /usr/include/c++/13/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 315 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In file included from /<>/src/cxx/libraries/prime/EpochTree.cc:7: /<>/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; | ^~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::set(unsigned int, unsigned int, const_iterator) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:162:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 162 | inline void set(unsigned i, unsigned j, const_iterator start) | ^~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtMap::set(unsigned int, unsigned int, const_iterator) [with T = double]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:165:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::set(const beep::EpochTime&, const_iterator) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:173:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 173 | inline void set(const EpochTime& tm, const_iterator start) | ^~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtMap::set(const beep::EpochTime&, const_iterator) [with T = double]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:176:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::setWithMin(unsigned int, unsigned int, const_iterator, const T&) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:188:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 188 | inline void setWithMin(unsigned i, unsigned j, const_iterator start, const T& lowerBound) | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::setWithMax(unsigned int, unsigned int, const_iterator, const T&) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:206:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 206 | inline void setWithMax(unsigned i, unsigned j, const_iterator start, const T& upperBound) | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::set(unsigned int, unsigned int, const_iterator) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:162:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 162 | inline void set(unsigned i, unsigned j, const_iterator start) | ^~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtMap::set(unsigned int, unsigned int, const_iterator) [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:165:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::set(const beep::EpochTime&, const_iterator) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:173:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 173 | inline void set(const EpochTime& tm, const_iterator start) | ^~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtMap::set(const beep::EpochTime&, const_iterator) [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:176:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::setWithMin(unsigned int, unsigned int, const_iterator, const T&) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:188:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 188 | inline void setWithMin(unsigned i, unsigned j, const_iterator start, const T& lowerBound) | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtMap::setWithMax(unsigned int, unsigned int, const_iterator, const T&) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:206:21: note: parameter passing for argument of type ‘beep::EpochPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 206 | inline void setWithMax(unsigned i, unsigned j, const_iterator start, const T& upperBound) | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::setWithMin(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator, const T&) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:438:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 438 | inline void setWithMin(unsigned i, unsigned j, unsigned p, unsigned q, | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::set(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:403:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 403 | inline void set(unsigned i, unsigned j, unsigned p, unsigned q, | ^~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtPtMap::set(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator) [with T = double]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:407:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::set(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:403:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 403 | inline void set(unsigned i, unsigned j, unsigned p, unsigned q, | ^~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtPtMap::set(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator) [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:407:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::setWithMax(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator, const T&) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:461:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 461 | inline void setWithMax(unsigned i, unsigned j, unsigned p, unsigned q, | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::setWithMin(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator, const T&) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:438:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 438 | inline void setWithMin(unsigned i, unsigned j, unsigned p, unsigned q, | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::setWithMax(unsigned int, unsigned int, unsigned int, unsigned int, const_iterator, const T&) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:461:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 461 | inline void setWithMax(unsigned i, unsigned j, unsigned p, unsigned q, | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::set(beep::EpochTime, beep::EpochTime, const_iterator) [with T = beep::Probability]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:418:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 418 | inline void set(EpochTime tm1, EpochTime tm2, const_iterator start) | ^~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtPtMap::set(beep::EpochTime, beep::EpochTime, const_iterator) [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:422:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function ‘void beep::EpochPtPtMap::set(beep::EpochTime, beep::EpochTime, const_iterator) [with T = double]’: /<>/src/cxx/libraries/prime/EpochPtMaps.hh:418:21: note: parameter passing for argument of type ‘beep::EpochPtPtMap::const_iterator’ {aka ‘std::vector >::const_iterator’} changed in GCC 7.1 418 | inline void set(EpochTime tm1, EpochTime tm2, const_iterator start) | ^~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::EpochPtPtMap::set(beep::EpochTime, beep::EpochTime, const_iterator) [with T = double]’ at /<>/src/cxx/libraries/prime/EpochPtMaps.hh:422:11: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/EpochTree.hh:7: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {beep::EpochPtSet}; _Tp = beep::EpochPtSet; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::EpochPtSet}; _Tp = beep::EpochPtSet; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::EpochPtSet; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::EpochTree::update()’ at /<>/src/cxx/libraries/prime/EpochTree.cc:79:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::EpochPtSet}; _Tp = beep::EpochPtSet; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::EpochPtSet; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::EpochTree::update()’ at /<>/src/cxx/libraries/prime/EpochTree.cc:98:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/NodeMap.cc [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/NodeNodeMap.cc [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/RandomTreeGenerator.cc [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/StrStrMap.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Tree.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreeAnalysis.cc [ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreeDiscretizer.cc [ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreeDiscretizers.cc [ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreeMCMC.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/BeepVector.hh:5, from /<>/src/cxx/libraries/prime/Tree.cc:7: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::RealVector::addElement(unsigned int, const beep::Real&)’ at /<>/src/cxx/libraries/prime/BeepVector.hh:306:17, inlined from ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ at /<>/src/cxx/libraries/prime/Tree.cc:517:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::RealVector::addElement(unsigned int, const beep::Real&)’ at /<>/src/cxx/libraries/prime/BeepVector.hh:306:17, inlined from ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ at /<>/src/cxx/libraries/prime/Tree.cc:521:21: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::RealVector::addElement(unsigned int, const beep::Real&)’ at /<>/src/cxx/libraries/prime/BeepVector.hh:306:17, inlined from ‘virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)’ at /<>/src/cxx/libraries/prime/Tree.cc:525:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/TreeDiscretizer.hh:6, from /<>/src/cxx/libraries/prime/TreeDiscretizer.cc:6: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::TreeDiscretizerOld::update()’ at /<>/src/cxx/libraries/prime/TreeDiscretizer.cc:84:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::TreeDiscretizerOld::update()’ at /<>/src/cxx/libraries/prime/TreeDiscretizer.cc:93:24: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::TreeDiscretizerOld::update()’ at /<>/src/cxx/libraries/prime/TreeDiscretizer.cc:109:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::TreeDiscretizerOld::update()’ at /<>/src/cxx/libraries/prime/TreeDiscretizer.cc:121:24: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreeIO.cc [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreeInputOutput.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/TreeDiscretizers.hh:6, from /<>/src/cxx/libraries/prime/TreeDiscretizers.cc:4: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘virtual void beep::StepSizeEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector >&) const’ at /<>/src/cxx/libraries/prime/TreeDiscretizers.cc:113:18: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘virtual void beep::StepSizeEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector >&) const’ at /<>/src/cxx/libraries/prime/TreeDiscretizers.cc:118:15: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘virtual void beep::StepSizeEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector >&) const’ at /<>/src/cxx/libraries/prime/TreeDiscretizers.cc:122:50: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘virtual void beep::EquiSplitEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector >&) const’ at /<>/src/cxx/libraries/prime/TreeDiscretizers.cc:54:18: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘virtual void beep::EquiSplitEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector >&) const’ at /<>/src/cxx/libraries/prime/TreeDiscretizers.cc:59:15: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘virtual void beep::EquiSplitEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector >&) const’ at /<>/src/cxx/libraries/prime/TreeDiscretizers.cc:63:50: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreeIOTraits.cc /<>/src/cxx/libraries/prime/TreeMCMC.cc: In constructor ‘beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const beep::Real&)’: /<>/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 /<>/src/cxx/libraries/prime/BranchSwapping.hh:5, from /<>/src/cxx/libraries/prime/TreeMCMC.hh:6, from /<>/src/cxx/libraries/prime/TreeMCMC.cc:1: /<>/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ /<>/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), | ^~~~ /<>/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ /<>/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), | ^~~~ /<>/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TreePerturbationEvent.cc /<>/src/cxx/libraries/prime/TreeInputOutput.cc: In member function ‘void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)’: /<>/src/cxx/libraries/prime/TreeInputOutput.cc:118:29: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null] 118 | buf[ bytes_read ]=NULL; | ^~~~ [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ConstRateModel.cc In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/BeepVector.hh:5: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::OrthologyMCMC::estimateOrthology(bool)’ at /<>/src/cxx/libraries/prime/TreeMCMC.cc:764:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::OrthologyMCMC::OrthologyMCMC(const beep::OrthologyMCMC&)’ at /<>/src/cxx/libraries/prime/TreeMCMC.cc:736:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44, inlined from ‘beep::OrthologyMCMC& beep::OrthologyMCMC::operator=(const beep::OrthologyMCMC&)’ at /<>/src/cxx/libraries/prime/TreeMCMC.cc:748:18: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Density2P_common.cc [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Density2P_positive.cc In file included from /<>/src/cxx/libraries/prime/Density2P_common.cc:5: /<>/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 /<>/src/cxx/libraries/prime/Density2P_common.cc:1: /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/Density2P_common.cc:6: /<>/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$. | ^~ /<>/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 /<>/src/cxx/libraries/prime/Density2P_common.cc:7: /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/Density2P_common.cc:8: /<>/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by ‘virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const’ 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/TreeIO.hh:10, from /<>/src/cxx/libraries/prime/TreeIO.cc:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const beep::Tree&}; _Tp = beep::Tree; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/Density2PMCMC.cc In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = beep::Tree; _Alloc = std::allocator]’, inlined from ‘std::vector beep::TreeIO::readAllBeepTrees(const beep::TreeIOTraits&, std::vector*, std::vector*)’ at /<>/src/cxx/libraries/prime/TreeIO.cc:274:14: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeRateMCMC.cc [ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/TreeInputOutput.hh:13, from /<>/src/cxx/libraries/prime/TreeInputOutput.cc:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const beep::Tree&}; _Tp = beep::Tree; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = beep::Tree; _Alloc = std::allocator]’, inlined from ‘std::vector beep::TreeInputOutput::readAllBeepTrees(beep::TreeIOTraits&, std::vector*, std::vector*)’ at /<>/src/cxx/libraries/prime/TreeInputOutput.cc:505:14: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeRateModel_common.cc [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeWeightHandler.cc /<>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function ‘void beep::EdgeRateMCMC_common::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]’: /<>/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); | ^~~~~~ /<>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable ‘rparam’ [-Wunused-variable] 105 | Real rparam = variance * (rtime + ltime); | ^~~~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeWeightMCMC.cc [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/GammaDensity.cc [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/InvGaussDensity.cc In file included from /<>/src/cxx/libraries/prime/EdgeWeightHandler.cc:1: /<>/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); | ^~~~ /<>/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 /<>/src/cxx/libraries/prime/Density2P_positive.hh:4, from /<>/src/cxx/libraries/prime/GammaDensity.hh:4, from /<>/src/cxx/libraries/prime/GammaDensity.cc:1: /<>/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; | ^~~~~~~~ /<>/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/LengthRateModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/LengthRateModel.cc /<>/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function ‘void beep::EdgeWeightMCMC::showCurrentTree()’: /<>/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 /<>/src/cxx/libraries/prime/InvGaussDensity.cc:1: /<>/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 /<>/src/cxx/libraries/prime/Density2P_positive.hh:4, from /<>/src/cxx/libraries/prime/InvGaussDensity.hh:4: /<>/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; | ^~~~~~~~ /<>/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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/LogNormDensity.cc [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/NormalDensity.cc [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/UniformDensity.cc In file included from /<>/src/cxx/libraries/prime/LogNormDensity.cc:1: /<>/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$. | ^~ In file included from /<>/src/cxx/libraries/prime/NormalDensity.cc:1: /<>/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /<>/src/cxx/libraries/prime/NormalDensity.hh:4: /<>/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; | ^~~~~~~~ /<>/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by ‘virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const’ 54 | Probability operator()(const Real& x) const; | ^~~~~~~~ [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/VarRateModel.cc In file included from /<>/src/cxx/libraries/prime/UniformDensity.hh:4, from /<>/src/cxx/libraries/prime/UniformDensity.cc:1: /<>/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; | ^~~~~~~~ /<>/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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SiteRateHandler.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/DummyMCMC.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MCMCModel.cc [ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/StdMCMCModel.cc In file included from /<>/src/cxx/libraries/prime/SiteRateHandler.cc:7: /<>/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. | ^~~ [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MCMCObject.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SimpleMCMC.cc [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SimpleMCMCPostSample.cc In file included from /<>/src/cxx/libraries/prime/StdMCMCModel.cc:5: /<>/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$. | ^~ In file included from /<>/src/cxx/libraries/prime/StdMCMCModel.cc:6: /<>/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ In file included from /<>/src/cxx/libraries/prime/Density2P_positive.hh:4, from /<>/src/cxx/libraries/prime/LogNormDensity.hh:4: /<>/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; | ^~~~~~~~ /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/StdMCMCModel.cc:7: /<>/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; | ^~~~~~~~ [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SimpleML.cc [ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/mcmc/MCMCSampler.cc /<>/src/cxx/libraries/prime/SimpleMCMC.cc: In member function ‘virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)’: /<>/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; | ^~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/mcmc/GSRSampler.cc [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SimpleObserver.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MpiMCMC.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MultiGSR.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MpiMultiGSR.cc [ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BDTreeGenerator.cc /<>/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function ‘virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)’: /<>/src/cxx/libraries/prime/MpiMultiGSR.cc:338:27: warning: operation on ‘i’ may be undefined [-Wsequence-point] 338 | p[++i] = geneFams[i]->initStateProb();//updateDataProbability(); | ^~~ /<>/src/cxx/libraries/prime/MpiMultiGSR.cc:338:27: warning: operation on ‘i’ may be undefined [-Wsequence-point] /<>/src/cxx/libraries/prime/MpiMultiGSR.cc:338:27: 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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BirthDeathMCMC.cc In file included from /usr/include/c++/13/map:62, from /<>/src/cxx/libraries/prime/Beep.hh:5, from /<>/src/cxx/libraries/prime/Probability.hh:14, from /<>/src/cxx/libraries/prime/BeepVector.hh:8, from /<>/src/cxx/libraries/prime/BDTreeGenerator.hh:4, from /<>/src/cxx/libraries/prime/BDTreeGenerator.cc:1: /usr/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = beep::Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘beep::Node* beep::BDTreeGenerator::generateV(beep::Node*)’ at /<>/src/cxx/libraries/prime/BDTreeGenerator.cc:155:9: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘beep::Node* beep::BDTreeGenerator::generateV(beep::Node*)’ at /<>/src/cxx/libraries/prime/BDTreeGenerator.cc:179:10: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘beep::Node* beep::BDTreeGenerator::generateX(beep::Node*, beep::Real)’ at /<>/src/cxx/libraries/prime/BDTreeGenerator.cc:237:14: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘virtual bool beep::BDTreeGenerator::generateTree(beep::Tree&, bool)’ at /<>/src/cxx/libraries/prime/BDTreeGenerator.cc:83:10: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘virtual bool beep::BDTreeGenerator::generateTree(beep::Tree&, bool)’ at /<>/src/cxx/libraries/prime/BDTreeGenerator.cc:98:25: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BirthDeathProbs.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc In file included from /usr/include/c++/13/vector:65, from /usr/include/c++/13/functional:64, from /usr/include/boost/utility/compare_pointees.hpp:15, from /usr/include/boost/optional/optional.hpp:61, from /usr/include/boost/optional.hpp:15, from /usr/include/boost/mpi/environment.hpp:18, from /<>/src/cxx/libraries/prime/MpiMultiGSR.hh:10, from /<>/src/cxx/libraries/prime/MpiMultiGSR.cc:6: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::SeriGSRvars*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::SeriGSRvars*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::SeriGSRvars*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::SeriGSRvars*; _Tp = beep::SeriGSRvars]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = beep::SeriGSRvars; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::SeriGSRvars; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44, inlined from ‘beep::SeriMultiGSRvars& beep::SeriMultiGSRvars::operator=(const beep::SeriMultiGSRvars&)’ at /<>/src/cxx/libraries/prime/MpiMultiGSR.cc:104:15: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::SeriGSRvars*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::SeriGSRvars*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::SeriGSRvars*; _Tp = beep::SeriGSRvars]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::SeriGSRvars; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::SeriMultiGSRvars::SeriMultiGSRvars(const beep::SeriMultiGSRvars&)’ at /<>/src/cxx/libraries/prime/MpiMultiGSR.cc:95:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {beep::SeriGSRvars}; _Tp = beep::SeriGSRvars; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::SeriGSRvars}; _Tp = beep::SeriGSRvars; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::SeriGSRvars; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::MpiMultiGSR::updateGvars(unsigned int)’ at /<>/src/cxx/libraries/prime/MpiMultiGSR.cc:223:17: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /<>/src/cxx/libraries/prime/BirthDeathMCMC.cc:1: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/BirthDeathMCMC.hh:23:9: note: by ‘beep::BirthDeathMCMC& beep::BirthDeathMCMC::operator=(const beep::BirthDeathMCMC&)’ 23 | class BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~ [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeDiscBDProbs.cc In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/BeepVector.hh:5, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /<>/src/cxx/libraries/prime/BirthDeathProbs.cc:5: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::BeepVector::BeepVector(const beep::BeepVector&) [with Type = beep::Probability]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:71:9, inlined from ‘beep::BirthDeathProbs::BirthDeathProbs(const beep::BirthDeathProbs&)’ at /<>/src/cxx/libraries/prime/BirthDeathProbs.cc:71:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::BeepVector::BeepVector(const beep::BeepVector&) [with Type = beep::Probability]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:71:9, inlined from ‘beep::BirthDeathProbs::BirthDeathProbs(const beep::BirthDeathProbs&)’ at /<>/src/cxx/libraries/prime/BirthDeathProbs.cc:72:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::BeepVector::BeepVector(const beep::BeepVector&) [with Type = beep::Probability]’ at /<>/src/cxx/libraries/prime/BeepVector.hh:71:9, inlined from ‘beep::BirthDeathProbs::BirthDeathProbs(const beep::BirthDeathProbs&)’ at /<>/src/cxx/libraries/prime/BirthDeathProbs.cc:73:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc In file included from /<>/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: /<>/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/BeepVector.hh:5, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const beep::Probability&}; _Tp = beep::Probability; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘const beep::Node* beep::DiscBirthDeathProbs::getConstLinValsForPath(std::vector >&, beep::DiscTree::Point, beep::DiscTree::Point, bool) const’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:190:18: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘const beep::Node* beep::DiscBirthDeathProbs::getConstLinValsForPath(std::vector >&, beep::DiscTree::Point, beep::DiscTree::Point, bool) const’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:193:17: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘const beep::Node* beep::DiscBirthDeathProbs::getConstLinValsForPath(std::vector >&, beep::DiscTree::Point, beep::DiscTree::Point, bool) const’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:203:18: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:65: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 315 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:324:40: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:345:35: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘beep::DiscBirthDeathProbs::DiscBirthDeathProbs(const beep::DiscBirthDeathProbs&)’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:58:24: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::DiscBirthDeathProbs::copyLeafBProbs(std::vector >&, unsigned int)’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:283:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void beep::DiscBirthDeathProbs::copyLeafBProbs(std::vector >&, unsigned int)’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:290:18: /usr/include/c++/13/bits/stl_vector.h:826:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 826 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::DiscBirthDeathProbs::calcBDProbs(const beep::Node*)’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:255:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::Probability}; _Tp = beep::Probability; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::DiscBirthDeathProbs::calcBDProbs(const beep::Node*)’ at /<>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:263:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EpochBDTMCMC.cc In file included from /<>/src/cxx/libraries/prime/Density2P_positive.hh:4, from /<>/src/cxx/libraries/prime/GammaDensity.hh:4, from /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /<>/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor ‘beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)’: /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: ‘beep::EdgeDiscGSR::m_calculatedAtAndBelow’ will be initialized after [-Wreorder] 588 | bool m_calculatedAtAndBelow; | ^~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: ‘bool beep::EdgeDiscGSR::m_calculatedAtBars’ [-Wreorder] 583 | bool m_calculatedAtBars; | ^~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, | ^~~~~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function ‘void beep::EdgeDiscGSR::convertDensitiesToProbabilities()’: /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable ‘xpt’ set but not used [-Wunused-but-set-variable] 485 | Point xpt = x.getPt(); | ^~~ /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable ‘parent’ [-Wunused-variable] 528 | Node *parent = u->getParent(); | ^~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function ‘beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)’: /<>/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/EpochBDTProbs.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EpochBDTProbs.cc [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EpochDLTRS.cc In file included from /<>/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /<>/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /<>/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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 /<>/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /<>/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; | ^~~~~~~~~~~~~~~~ /<>/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; | ^~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /<>/src/cxx/libraries/prime/EpochDLTRS.cc:3: /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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 /<>/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /<>/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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 /<>/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /<>/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; | ^~~~~~~~~~~~~~~~ /<>/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; | ^~~~~~~ /<>/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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/GammaMap.cc [ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/GuestTreeModel.cc In file included from /<>/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /<>/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; | ^~~~~~~~~~~~~~~~ /<>/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; | ^~~~~~~ /<>/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 /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/BeepVector.hh:5, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /<>/src/cxx/libraries/prime/EpochBDTProbs.cc:6: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::EpochBDTProbs::appendInitVals(realvec&) const’ at /<>/src/cxx/libraries/prime/EpochBDTProbs.cc:239:10: /usr/include/c++/13/bits/stl_vector.h:1437:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1437 | _M_fill_insert(begin() + __offset, __n, __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EnumerateReconciliationModel.cc [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/BeepVector.hh:5, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /<>/src/cxx/libraries/prime/GuestTreeModel.cc:4: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {const vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >*, vector >, allocator > > > >; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21, inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::vector >*; _ForwardIterator = std::vector >*; bool _TrivialValueTypes = false]’ at /usr/include/c++/13/bits/stl_uninitialized.h:137:32, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = vector >*; _ForwardIterator = vector >*; _Tp = vector >]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::vector >; _Alloc = std::allocator > >]’ at /usr/include/c++/13/bits/vector.tcc:257:35, inlined from ‘beep::NodeNodeMap& beep::NodeNodeMap::operator=(const beep::NodeNodeMap&) [with T = std::vector >]’ at /<>/src/cxx/libraries/prime/NodeNodeMap.hh:38:9, inlined from ‘beep::NodeNodeMap& beep::NodeNodeMap::operator=(const beep::NodeNodeMap&) [with T = std::vector >]’ at /<>/src/cxx/libraries/prime/NodeNodeMap.hh:33:5, inlined from ‘beep::GuestTreeModel& beep::GuestTreeModel::operator=(const beep::GuestTreeModel&)’ at /<>/src/cxx/libraries/prime/GuestTreeModel.cc:79:10: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::NodeNodeMap::NodeNodeMap(const beep::NodeNodeMap&) [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/NodeNodeMap.hh:28:2, inlined from ‘beep::GuestTreeModel::GuestTreeModel(const beep::GuestTreeModel&)’ at /<>/src/cxx/libraries/prime/GuestTreeModel.cc:55:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/fastGEM.cc In file included from /<>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /<>/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:7, from /<>/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc:1: /<>/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); | ^~~~~~~~ /<>/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 | ^~~~~~~~~~~~~~~~~~~~~~~ /<>/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); | ^~~~~~~~ /<>/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, | ^~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/LambdaMap.cc [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MaxReconciledTreeModel.cc In file included from /<>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /<>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: /<>/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); | ^~~~~~~~ /<>/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 /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:5: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘beep::fastGEM_BirthDeathProbs::fastGEM_BirthDeathProbs(beep::Tree&, unsigned int, std::vector >*, const beep::Real&, const beep::Real&)’ at /<>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:30:24: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/PerturbationObservable.cc In file included from /<>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /<>/src/cxx/libraries/prime/fastGEM.hh:8, from /<>/src/cxx/libraries/prime/fastGEM.cc:2: /<>/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); | ^~~~~~~~ /<>/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 | ^~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/fastGEM.cc: In member function ‘unsigned int beep::fastGEM::calcMaxProb(unsigned int)’: /<>/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); | ^~~~~~~~~~~ /<>/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printSa()’: /<>/src/cxx/libraries/prime/fastGEM.cc:1298:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1298 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLb()’: /<>/src/cxx/libraries/prime/fastGEM.cc:1325:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1325 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/fastGEM.cc: In member function ‘void beep::fastGEM::printLt()’: /<>/src/cxx/libraries/prime/fastGEM.cc:1356:10: warning: variable ‘zeroTotalQuotient’ set but not used [-Wunused-but-set-variable] 1356 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciledTreeModel.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciliationModel.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciliationSampler.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciliationTimeModel.cc In file included from /<>/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /<>/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$. | ^~ [ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc /<>/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function ‘void beep::ReconciliationSampler::setAttributesAndProbabilities()’: /<>/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 161 | Probability p = calculateDataProbability(); | ^ /<>/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function ‘std::string beep::ReconciliationTimeModel::table4os() const’: /<>/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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/BeepVector.hh:5, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /<>/src/cxx/libraries/prime/ReconciliationSampler.cc:5: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {const vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >*, vector >, allocator > > > >; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21, inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::vector >*; _ForwardIterator = std::vector >*; bool _TrivialValueTypes = false]’ at /usr/include/c++/13/bits/stl_uninitialized.h:137:32, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = vector >*; _ForwardIterator = vector >*; _Tp = vector >]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::vector >; _Alloc = std::allocator > >]’ at /usr/include/c++/13/bits/vector.tcc:257:35: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/DLRSOrthoCalculator.cc /<>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function ‘const std::string beep::ReconciliationTimeSampler::table4os() const’: /<>/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; | ^~~~~~~ [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SetOfNodes.cc /<>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor ‘beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const std::string&)’: /<>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: ‘beep::ReconciliationTreeGenerator::R’ is initialized with itself [-Winit-self] 31 | ReconciliationTreeGenerator:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TopTimeMCMC.cc In file included from /<>/src/cxx/libraries/prime/Density2P_positive.hh:4, from /<>/src/cxx/libraries/prime/GammaDensity.hh:4, from /<>/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:20, from /<>/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: /<>/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; | ^~~~~~~~ /<>/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; | ^~~~~~~~ [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridBranchSwapping.cc [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridTree.cc In file included from /<>/src/cxx/libraries/prime/HybridTree.hh:4, from /<>/src/cxx/libraries/prime/HybridBranchSwapping.cc:3: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /<>/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; | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by ‘std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const’ 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /<>/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:22: /<>/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:11: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridTreeIO.cc In file included from /<>/src/cxx/libraries/prime/HybridTree.hh:4, from /<>/src/cxx/libraries/prime/HybridTree.cc:1: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /<>/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; | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by ‘std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const’ 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridTreeInputOutput.cc In file included from /<>/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /<>/src/cxx/libraries/prime/HybridTreeIO.cc:1: /<>/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); | ^~~~~~~~ /<>/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 /usr/include/c++/13/map:62, from /<>/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:13: /usr/include/c++/13/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.cc: In member function ‘beep::Tree& beep::HybridTree::getBinaryTree() const’: /<>/src/cxx/libraries/prime/HybridTree.cc:367:40: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] 367 | if(rootNode && bTree.getRootNode() == false) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Alloc>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair, double>; _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’ at /usr/include/c++/13/bits/stl_map.h:860:27, inlined from ‘std::map, double> DLRSOrthoCalculator::getOrthoEstimates()’ at /<>/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:114:35: /usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type ‘std::map, double>::const_iterator’ {aka ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’} changed in GCC 7.1 640 | return _M_t._M_emplace_hint_unique(__pos, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/LambdaMap.hh:4, from /<>/src/cxx/libraries/prime/GammaMap.hh:4, from /<>/src/cxx/libraries/prime/HybridTreeIO.cc:4: /<>/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 /<>/src/cxx/libraries/prime/HybridTreeIO.cc:5: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/LambdaMap.hh:4, from /<>/src/cxx/libraries/prime/GammaMap.hh:4, from /<>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:4: /<>/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 /<>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:5: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/TreeIO.hh:10: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const beep::HybridTree&}; _Tp = beep::HybridTree; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = beep::HybridTree; _Alloc = std::allocator]’, inlined from ‘std::vector beep::HybridTreeIO::readAllHybridTrees(beep::TreeIOTraits, std::vector*, std::vector*)’ at /<>/src/cxx/libraries/prime/HybridTreeIO.cc:236:14: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/TreeInputOutput.hh:13, from /<>/src/cxx/libraries/prime/HybridTreeInputOutput.hh:4, from /<>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const beep::HybridTree&}; _Tp = beep::HybridTree; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = beep::HybridTree; _Alloc = std::allocator]’, inlined from ‘std::vector beep::HybridTreeInputOutput::readAllHybridTrees(beep::TreeIOTraits&, std::vector*, std::vector*)’ at /<>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:130:14: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridBDTreeGenerator.cc In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/LambdaMap.hh:4, from /<>/src/cxx/libraries/prime/GammaMap.hh:4, from /<>/src/cxx/libraries/prime/TreeGenerator.hh:4, from /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:5, from /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:1: /<>/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 /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:6: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /usr/include/c++/13/map:62, from /<>/src/cxx/libraries/prime/Beep.hh:5, from /<>/src/cxx/libraries/prime/PRNG.hh:4, from /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:4: /usr/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = beep::Node*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void beep::BDHybridTreeGenerator::generateV(unsigned int)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:182:9: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /<>/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:5: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: note: by ‘virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)’ 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); | ^~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /<>/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 /<>/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:7: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, from /<>/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:7, from /<>/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:1: /<>/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); | ^~~~~~~~ /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: warning: ‘virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)’ was hidden [-Woverloaded-virtual=] /<>/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:22:9: note: by ‘beep::BirthDeathInHybridMCMC& beep::BirthDeathInHybridMCMC::operator=(const beep::BirthDeathInHybridMCMC&)’ 22 | class BirthDeathInHybridMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void beep::BDHybridTreeGenerator::generateX(unsigned int, beep::Real)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:246:10: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void beep::BDHybridTreeGenerator::generateX(unsigned int, beep::Real)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:290:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void beep::BDHybridTreeGenerator::generateX(unsigned int, beep::Real)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:307:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void beep::BDHybridTreeGenerator::generateX(unsigned int, beep::Real)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:318:16: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void beep::BDHybridTreeGenerator::generateX(unsigned int, beep::Real)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:319:16: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void beep::BDHybridTreeGenerator::generateX(unsigned int, beep::Real)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:327:14: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /<>/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 /<>/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:6: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = beep::Node*; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘bool beep::BDHybridTreeGenerator::generateHybridTree(beep::HybridTree&)’ at /<>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:97:22: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/BDTreeGenerator.hh:4, from /<>/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:4, from /<>/src/cxx/libraries/prime/HybridBDTreeGenerator.cc:1: /<>/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 /<>/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:5: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridGuestTreeModel.cc [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridHostTreeMCMC.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc In file included from /<>/src/cxx/libraries/prime/NodeNodeMap.hh:7, from /<>/src/cxx/libraries/prime/HybridGuestTreeModel.hh:4, from /<>/src/cxx/libraries/prime/HybridGuestTreeMCMC.hh:4, from /<>/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:1: /<>/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 /<>/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:4: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /<>/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; | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by ‘std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const’ 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/BirthDeathProbs.hh:9, from /<>/src/cxx/libraries/prime/HybridGuestTreeModel.cc:4: /<>/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 /<>/src/cxx/libraries/prime/HybridGuestTreeModel.cc:8: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /<>/src/cxx/libraries/prime/HybridTree.hh:4, from /<>/src/cxx/libraries/prime/HybridHostTreeMCMC.hh:5, from /<>/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:1: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /<>/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /<>/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:6: /<>/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); | ^~~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/HybridTree.hh:4, from /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc:4: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: /<>/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 /<>/src/cxx/libraries/prime/NormalDensity.hh:4: /<>/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; | ^~~~~~~~ /<>/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; | ^~~~~~~~ [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/utility/compare_pointees.hpp:15, from /usr/include/boost/optional/optional.hpp:61, from /usr/include/boost/optional.hpp:15, from /usr/include/boost/mpi/environment.hpp:18, from /<>/src/cxx/libraries/prime/Probability.hh:4, from /<>/src/cxx/libraries/prime/ProbabilityModel.hh:7, from /<>/src/cxx/libraries/prime/HybridHostTreeModel.hh:4, from /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::HybridHostTreeModel::setMaxGhosts(unsigned int)’ at /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc:251:16: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::HybridHostTreeModel::setMaxGhosts(unsigned int)’ at /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc:252:16: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::HybridHostTreeModel::setMaxGhosts(unsigned int)’ at /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc:253:14: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void beep::HybridHostTreeModel::setMaxGhosts(unsigned int)’ at /<>/src/cxx/libraries/prime/HybridHostTreeModel.cc:254:14: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/BeepVector.hh:5: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {const vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >*, vector >, allocator > > > >; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector >; _Args = {vector >&}]’ at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:120:21, inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::vector >*; _ForwardIterator = std::vector >*; bool _TrivialValueTypes = false]’ at /usr/include/c++/13/bits/stl_uninitialized.h:137:32, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = vector >*; _ForwardIterator = vector >*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = vector >*; _ForwardIterator = vector >*; _Tp = vector >]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = std::vector >; _Alloc = std::allocator > >]’ at /usr/include/c++/13/bits/vector.tcc:257:35: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*; _Tp = beep::Probability]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::NodeNodeMap::NodeNodeMap(const beep::NodeNodeMap&) [with T = beep::Probability]’ at /<>/src/cxx/libraries/prime/NodeNodeMap.hh:28:2, inlined from ‘beep::HybridGuestTreeModel::HybridGuestTreeModel(const beep::HybridGuestTreeModel&)’ at /<>/src/cxx/libraries/prime/HybridGuestTreeModel.cc:60:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/CacheSubstitutionModel.cc [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/LambdaMap.hh:4, from /<>/src/cxx/libraries/prime/GammaMap.hh:4, from /<>/src/cxx/libraries/prime/ReconciliationModel.hh:8, from /<>/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /<>/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.hh:4, from /<>/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:1: /<>/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 /<>/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:3: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /<>/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, from /<>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: /usr/include/c++/13/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 /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MatrixCache.cc [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/TransitionHandler.cc In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/LambdaMap.hh:4, from /<>/src/cxx/libraries/prime/GammaMap.hh:4, from /<>/src/cxx/libraries/prime/ReconciliationModel.hh:8, from /<>/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1: /<>/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 /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:4: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/BeepVector.hh:5: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::GuestTreeModel*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::ReconciledTreeTimeModel*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::GuestTreeModel*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::GuestTreeModel*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::GuestTreeModel*; _Tp = beep::GuestTreeModel]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = beep::GuestTreeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::GuestTreeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44, inlined from ‘beep::EnumHybridGuestTreeModel& beep::EnumHybridGuestTreeModel::operator=(const beep::EnumHybridGuestTreeModel&)’ at /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:56:15: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::ReconciledTreeTimeModel*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::ReconciledTreeTimeModel*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::ReconciledTreeTimeModel*; _Tp = beep::ReconciledTreeTimeModel]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44, inlined from ‘beep::EnumHybridGuestTreeModel& beep::EnumHybridGuestTreeModel::operator=(const beep::EnumHybridGuestTreeModel&)’ at /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:57:18: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/CacheSubstitutionModel.cc:4: /<>/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); | ^~~~ /<>/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 /<>/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /<>/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 /usr/include/c++/13/vector:72: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {beep::ReconciledTreeTimeModel}; _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {beep::GuestTreeModel}; _Tp = beep::GuestTreeModel; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::GuestTreeModel*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::GuestTreeModel*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::GuestTreeModel*; _Tp = beep::GuestTreeModel]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::GuestTreeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::EnumHybridGuestTreeModel::EnumHybridGuestTreeModel(const beep::EnumHybridGuestTreeModel&)’ at /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:40:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::ReconciledTreeTimeModel*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::ReconciledTreeTimeModel*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::ReconciledTreeTimeModel*; _Tp = beep::ReconciledTreeTimeModel]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::EnumHybridGuestTreeModel::EnumHybridGuestTreeModel(const beep::EnumHybridGuestTreeModel&)’ at /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:41:7: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:5: /<>/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; | ^~~~~ /<>/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 /<>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:4: /<>/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); | ^~~~ /<>/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 /<>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /<>/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 member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::ReconciledTreeTimeModel}; _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::EnumHybridGuestTreeModel::inits()’ at /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:131:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {beep::GuestTreeModel}; _Tp = beep::GuestTreeModel; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = beep::GuestTreeModel; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘void beep::EnumHybridGuestTreeModel::inits()’ at /<>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:140:22: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SeqIO.cc [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SequenceGenerator.cc [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SequenceType.cc In file included from /usr/include/c++/13/map:62, from /<>/src/cxx/libraries/prime/Beep.hh:5, from /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:7: /usr/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::F81(std::map)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:310:23: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::F81(std::map)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:311:23: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::F81(std::map)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:312:23: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::F81(std::map)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:313:23: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::create(std::string, std::map*)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:26:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::create(std::string, std::map*)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:27:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::create(std::string, std::map*)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:28:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::create(std::string, std::map*)’ at /<>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:29:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/SequenceGenerator.hh:10, from /<>/src/cxx/libraries/prime/SequenceGenerator.cc:4: /<>/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); | ^~~~ /<>/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 /<>/src/cxx/libraries/prime/SequenceGenerator.hh:15: /<>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SequenceData.cc In file included from /usr/include/c++/13/vector:65, from /<>/src/cxx/libraries/prime/SequenceGenerator.hh:4: /usr/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*]’: /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*; _Tp = beep::MatrixTransitionHandler]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = beep::MatrixTransitionHandler; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::MatrixTransitionHandler; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:238:44, inlined from ‘beep::SequenceGenerator& beep::SequenceGenerator::operator=(const beep::SequenceGenerator&)’ at /<>/src/cxx/libraries/prime/SequenceGenerator.cc:66:9: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*; _Tp = beep::MatrixTransitionHandler]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::MatrixTransitionHandler; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from ‘beep::SequenceGenerator::SequenceGenerator(const beep::SequenceGenerator&)’ at /<>/src/cxx/libraries/prime/SequenceGenerator.cc:51:8: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SubstitutionModel.cc /<>/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 /<>/src/cxx/libraries/prime/SequenceType.cc:8: /<>/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a ‘friend’ 56 | friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); | ^~~~~~~~ [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/SubstitutionMCMC.cc /<>/src/cxx/libraries/prime/SequenceData.cc: In member function ‘std::map beep::SequenceData::getBaseFrequencies()’: /<>/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++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ /<>/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 ‘unsigned int’} [-Wsign-compare] 303 | for (int j = 0; j < seq.length(); j++) { | ~~^~~~~~~~~~~~~~ In file included from /<>/src/cxx/libraries/prime/SubstitutionModel.cc:4: /<>/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); | ^~~~ /<>/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 /<>/src/cxx/libraries/prime/SubstitutionModel.cc:9: /<>/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. | ^~~ [ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/LA_Vector.cc In file included from /usr/include/c++/13/map:62, from /<>/src/cxx/libraries/prime/SequenceData.cc:2: /usr/include/c++/13/bits/stl_tree.h: In function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from /<>/src/cxx/libraries/prime/SequenceData.cc:6: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/libraries/prime/LA_Matrix.cc In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:289:35: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:291:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:292:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:293:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:294:22: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:306:34: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:308:34: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:311:34: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:314:34: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:325:37: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:325:50: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:325:63: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:325:76: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:330:55: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map beep::SequenceData::getBaseFrequencies()’ at /<>/src/cxx/libraries/prime/SequenceData.cc:330:34: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && 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-Wl,-rpath,/usr/lib/arm-linux-gnueabihf/liblapack.so:/usr/lib/arm-linux-gnueabihf/libblas.so:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../sfile/libprime-phylo-sfile.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 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 '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/applications/primeDTLSR /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/applications/primeDLRS /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 82%] Generating cmdline.c, cmdline.h make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Generating cmdline.c, cmdline.h cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/gengetopt -i /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build [ 83%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR -I/<>/src/cxx/applications/primeDTLSR -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/applications/primeDTLSR/idolatrous.cc cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/applications/primeGEM /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake "--color=" [ 83%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS -I/<>/src/cxx/applications/primeDLRS -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/applications/primeDLRS/primeDLRS.cc cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/tools/treesize /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 83%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/<>/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/applications/primeGEM/troyo.cc [ 83%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/<>/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/tools/treesize/treesize.cc In file included from /<>/src/cxx/libraries/prime/HybridTree.hh:4, from /<>/src/cxx/tools/treesize/treesize.cc:8: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /<>/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; | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/src/cxx/tools/treesize/treesize.cc: In function ‘int main(int, char**)’: /<>/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) | ^ /<>/src/cxx/tools/treesize/treesize.cc:90:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 90 | catch (AnError e) { | ^ [ 84%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/<>/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c [ 85%] Linking CXX executable treesize cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so In file included from /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:9: /<>/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); | ^~~~ /<>/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 /<>/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /<>/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /<>/src/cxx/applications/primeDTLSR/idolatrous.cc: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 /<>/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /<>/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:13: /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~ /<>/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; | ^~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/Density2P_positive.hh:4, from /<>/src/cxx/libraries/prime/GammaDensity.hh:4, from /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:15: /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:16: /<>/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$ | ^~ /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:17: /<>/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$. | ^~ make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 85%] 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 '/<>/obj-arm-linux-gnueabihf' In file included from /<>/src/cxx/libraries/prime/Density2P_positive.hh:4, from /<>/src/cxx/libraries/prime/GammaDensity.hh:4, from /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, from /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:9: /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: /<>/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++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /<>/src/cxx/libraries/prime/BeepOption.hh:4, from /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 42 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)’: /<>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 64 | std::iterator(), | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 85%] Generating cmdline.c, cmdline.h cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/gengetopt -i /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree In file included from /<>/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, from /<>/src/cxx/applications/primeGEM/troyo.cc:2: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/BirthDeathMCMC.hh:23:9: note: by ‘beep::BirthDeathMCMC& beep::BirthDeathMCMC::operator=(const beep::BirthDeathMCMC&)’ 23 | class BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~ cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/tools/showtree /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake "--color=" In file included from /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:10: /<>/src/cxx/libraries/prime/EdgeWeightHandler.hh: At global scope: /<>/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); | ^~~~ /<>/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 /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:13: /<>/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$ | ^~ /<>/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; | ^~~~~~~~ /<>/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 /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:14: /<>/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 /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:23: /<>/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. | ^~~ make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/<>/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/tools/showtree/showtree.cc /<>/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 /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:28: /<>/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by ‘virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const’ 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ In file included from /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /<>/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. | ^~~ /<>/src/cxx/applications/primeGEM/troyo.cc: In function ‘int main(int, char**)’: /<>/src/cxx/applications/primeGEM/troyo.cc:197:25: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 197 | catch(AnError e) | ^ /<>/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 /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:28: /<>/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; | ^~~~~~~~ /<>/src/cxx/applications/primeDTLSR/idolatrous.cc: In function ‘int main(int, char**)’: /<>/src/cxx/applications/primeDTLSR/idolatrous.cc:172:91: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 172 | pair edgeRateMeanVar = Options.getDoubleX2("EdgeRateParams"); | ^ In file included from /<>/src/cxx/libraries/prime/HybridTreeIO.hh:4, from /<>/src/cxx/tools/showtree/showtree.cc:3: /<>/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); | ^~~~~~~~ /<>/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 /<>/src/cxx/libraries/prime/HybridTree.hh:4, from /<>/src/cxx/tools/showtree/showtree.cc:4: /<>/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); | ^~~~~~~~ /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /<>/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; | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/src/cxx/tools/showtree/showtree.cc: In function ‘void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)’: /<>/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; | ^~ /<>/src/cxx/tools/showtree/showtree.cc: In function ‘int main(int, char**)’: /<>/src/cxx/tools/showtree/showtree.cc:174:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 174 | if(args_info.tree_number_arg >= Tvec.size()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /<>/src/cxx/applications/primeDLRS/primeDLRS.cc: In function ‘int main(int, char**)’: /<>/src/cxx/applications/primeDLRS/primeDLRS.cc:101:65: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 101 | pair bdr = Options.getDoubleX2("BDRates"); | ^ /<>/src/cxx/tools/showtree/showtree.cc:198:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 198 | catch (AnError e) | ^ [ 87%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/<>/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.c [ 87%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/<>/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.c [ 87%] Linking CXX executable primeGEM cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so [ 88%] Linking CXX executable showtree cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Built target primeGEM make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 89%] Generating cmdline.c, cmdline.h cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/tools/reconcile /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 90%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/<>/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/tools/reconcile/Rootalyzer.cc make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 90%] Built target showtree make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 91%] Generating cmdline.c, cmdline.h cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/gengetopt -i /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/tools/reroot /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 91%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/<>/src/cxx/tools/reroot -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/tools/reroot/reroot.cc [ 92%] Linking CXX executable primeDTLSR cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:/usr/lib/arm-linux-gnueabihf/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 [ 93%] Linking CXX executable primeDLRS cd /<>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:/usr/lib/arm-linux-gnueabihf/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target primeDTLSR make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Generating cmdline.c, cmdline.h cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/tools/tree2leafnames /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 94%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/<>/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/tools/tree2leafnames/tree2leafnames.cc make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 94%] Built target primeDLRS make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 94%] Generating cmdline.c, cmdline.h cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/tools/chainsaw /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 95%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/<>/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/tools/chainsaw/chainsaw.cc [ 95%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/<>/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/src/cxx/tools/reconcile/reconcile.cc In file included from /<>/src/cxx/tools/tree2leafnames/tree2leafnames.cc:7: /<>/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 /<>/src/cxx/tools/tree2leafnames/tree2leafnames.cc:9: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /<>/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; | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/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, | ^~~~~~~~~~ /<>/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function ‘int main(int, char**)’: /<>/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) | ^ /<>/src/cxx/tools/tree2leafnames/tree2leafnames.cc:95:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 95 | catch (AnError e) { | ^ In file included from /<>/src/cxx/libraries/prime/BeepVector.hh:13, from /<>/src/cxx/libraries/prime/BranchSwapping.hh:5, from /<>/src/cxx/tools/reroot/reroot.cc:10: /<>/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 /<>/src/cxx/tools/reroot/reroot.cc:14: /<>/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by ‘beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)’ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ /<>/src/cxx/tools/reroot/reroot.cc: In function ‘int main(int, char**)’: /<>/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) | ^ /<>/src/cxx/tools/reroot/reroot.cc:181:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 181 | catch (AnError e) { | ^ [ 96%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/<>/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c [ 96%] Linking CXX executable tree2leafnames cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target tree2leafnames [ 97%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/<>/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.c [ 97%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/<>/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c /<>/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)’: /<>/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) | ^ /<>/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘beep::Tree ReadHostTree(gengetopt_args_info&)’: /<>/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) | ^ /<>/src/cxx/tools/chainsaw/chainsaw.cc: In function ‘int main(int, char**)’: /<>/src/cxx/tools/chainsaw/chainsaw.cc:163:24: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 163 | catch (AnError e) { | ^ /<>/src/cxx/tools/reconcile/reconcile.cc: In function ‘int main(int, char**)’: /<>/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"; | ^~~~~~~~~ /<>/src/cxx/tools/chainsaw/chainsaw.cc:188:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 188 | catch (AnError e) { | ^ /<>/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type ‘class beep::AnError’ by value [-Wcatch-value=] 128 | catch (AnError e) { | ^ /<>/src/cxx/tools/reconcile/reconcile.cc: In function ‘void populateGsMap(beep::Tree, beep::StrStrMap&)’: /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/<>/src/cxx/tools/reroot -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<>/src/cxx/libraries -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -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 /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.c [ 99%] Linking CXX executable reroot cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Built target reroot [100%] Linking CXX executable chainsaw cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so [100%] Linking CXX executable reconcile cd /<>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/prime-phylo-1.0.11-10ubuntu1 -fpermissive -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -Wreorder -Wall -fexceptions -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.83.0 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target chainsaw make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target reconcile make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' dh_auto_test -a -O--buildsystem=cmake create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=cmake dh_prep -a -O--buildsystem=cmake dh_auto_install --destdir=debian/prime-phylo/ -a -O--buildsystem=cmake cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<>/debian/prime-phylo AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Debug" -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/chainsaw.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/primeDLRS.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/primeGEM.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/reconcile.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/reroot.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/showtree.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1 -- Installing: /<>/debian/prime-phylo/usr/share/man/man1/treesize.1 -- Installing: /<>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/primeGEM -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/primeDTLSR -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/primeDLRS -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/treesize -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/showtree -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/reconcile -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/reroot -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/tree2leafnames -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/chainsaw -- Set non-toolchain portion of runtime path of "/<>/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo" -- Installing: /<>/debian/prime-phylo/usr/bin/mcmc_analysis make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' dh_installdocs -a -O--buildsystem=cmake dh_installchangelogs -a -O--buildsystem=cmake dh_installexamples -a -O--buildsystem=cmake dh_installman -a -O--buildsystem=cmake dh_installsystemduser -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake debugedit: debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so: Unknown DWARF DW_FORM_0x1f20 9292387a4ef34f37bd93962cd34e4212cacc8462 debugedit: debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so: Unknown DWARF DW_FORM_0x1f21 1fa0ceeb90a5d35cd1a26e972a54b532e5666e7e debugedit: debian/prime-phylo/usr/bin/showtree: Unknown DWARF DW_FORM_0x1f21 b679b3bcb4c4fade1315e7736c511a2776f6e323 debugedit: debian/prime-phylo/usr/bin/primeDTLSR: Unknown DWARF DW_FORM_0x1f21 6b33bedec6801a8135e81dcbb97027841a996cbd debugedit: debian/prime-phylo/usr/bin/tree2leafnames: Unknown DWARF DW_FORM_0x1f21 64f19a2453f041046868d29ccc0bebb71f53dc2d debugedit: debian/prime-phylo/usr/bin/reconcile: Unknown DWARF DW_FORM_0x1f21 2bdf725f356700498a718a91fa5d9925ac7929c7 debugedit: debian/prime-phylo/usr/bin/primeDLRS: Unknown DWARF DW_FORM_0x1f21 eea5f539eb25db9b2646fd117cbcf43408b4cf9d debugedit: debian/prime-phylo/usr/bin/chainsaw: Unknown DWARF DW_FORM_0x1f21 56844bdb4b61298c27fe4597161804310451fb02 debugedit: debian/prime-phylo/usr/bin/treesize: Unknown DWARF DW_FORM_0x1f21 9e1da17b4ce3db361d2acad33db4077bc2b02941 debugedit: debian/prime-phylo/usr/bin/primeGEM: Unknown DWARF DW_FORM_0x1f21 27877e29dfc2dc959ad0895f75cde67964e741b1 debugedit: debian/prime-phylo/usr/bin/reroot: Unknown DWARF DW_FORM_0x1f20 a89bbaf0d1d55bac7eb638bcbe41211a4e342750 debian/rules override_dh_makeshlibs make[1]: Entering directory '/<>' dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so make[1]: Leaving directory '/<>' dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/reconcile contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/reroot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeDTLSR contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeDLRS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake INFO: pkgstriptranslations version 154 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-10ubuntu1_armhf.deb'. dpkg-genbuildinfo --build=any -O../prime-phylo_1.0.11-10ubuntu1_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../prime-phylo_1.0.11-10ubuntu1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-04-11T22:30:49Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ prime-phylo_1.0.11-10ubuntu1_armhf.changes: ------------------------------------------- Format: 1.8 Date: Thu, 11 Apr 2024 16:13:48 -0600 Source: prime-phylo Binary: prime-phylo Built-For-Profiles: noudeb Architecture: armhf Version: 1.0.11-10ubuntu1 Distribution: noble Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Zixing Liu Description: prime-phylo - bayesian estimation of gene trees taking the species tree into ac Launchpad-Bugs-Fixed: 2061032 Changes: prime-phylo (1.0.11-10ubuntu1) noble; urgency=medium . * debian/patches/fix-ftbfs-with-gcc13.patch: Fix missing headers and missing prototypes. Closes LP: #2061032. Checksums-Sha1: d457d8c86158e7dd4810975087612a6b4f868da9 9439 prime-phylo_1.0.11-10ubuntu1_armhf.buildinfo 1c489f48e92a1eb14010b32723fbecdefe028eb3 804298 prime-phylo_1.0.11-10ubuntu1_armhf.deb Checksums-Sha256: ae66553c879bb4652afa8a1f33e544f2b56e6128094e29d5b14ade90ae31d87c 9439 prime-phylo_1.0.11-10ubuntu1_armhf.buildinfo 3c2fd9f7f0678b874ef60e64c71032013b9168be994a4db9871e7f90ec56dc35 804298 prime-phylo_1.0.11-10ubuntu1_armhf.deb Files: b524e658be67dfbde3f60e5afdc38776 9439 science optional prime-phylo_1.0.11-10ubuntu1_armhf.buildinfo 59cb3ca0c1a8f2ec346e9312dddb1cae 804298 science optional prime-phylo_1.0.11-10ubuntu1_armhf.deb Original-Maintainer: Debian Med Packaging Team /<>/prime-phylo_1.0.11-10ubuntu1_armhf.changes.new could not be renamed to /<>/prime-phylo_1.0.11-10ubuntu1_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: prime-phylo Binary: prime-phylo Architecture: armhf Version: 1.0.11-10ubuntu1 Checksums-Md5: 59cb3ca0c1a8f2ec346e9312dddb1cae 804298 prime-phylo_1.0.11-10ubuntu1_armhf.deb Checksums-Sha1: 1c489f48e92a1eb14010b32723fbecdefe028eb3 804298 prime-phylo_1.0.11-10ubuntu1_armhf.deb Checksums-Sha256: 3c2fd9f7f0678b874ef60e64c71032013b9168be994a4db9871e7f90ec56dc35 804298 prime-phylo_1.0.11-10ubuntu1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Thu, 11 Apr 2024 22:30:47 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.137ubuntu1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu2), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3build1), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-arm-linux-gnueabihf (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), bison (= 2:3.8.2+dfsg-1build2), bsdextrautils (= 2.39.3-9ubuntu6), bsdutils (= 1:2.39.3-9ubuntu6), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), cmake (= 3.28.3-1build6), cmake-data (= 3.28.3-1build6), coreutils (= 9.4-3ubuntu6), cpp (= 4:13.2.0-7ubuntu2), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), cpp-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu2), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1build1), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5build1), flex (= 2.6.4-8.2build1), g++ (= 4:13.2.0-7ubuntu2), g++-13 (= 13.2.0-23ubuntu3), g++-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), g++-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu2), gcc (= 4:13.2.0-7ubuntu2), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu2), gengetopt (= 2.23+dfsg1-1), gettext (= 0.21-14ubuntu2), gettext-base (= 0.21-14ubuntu2), gfortran (= 4:13.2.0-7ubuntu2), gfortran-13 (= 13.2.0-23ubuntu3), gfortran-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), gfortran-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu2), grep (= 3.11-4build1), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu3), hostname (= 3.23+nmu2ubuntu2), ibverbs-providers (= 50.0-2build2), icu-devtools (= 74.2-1ubuntu3), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1build1), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.2-2), libasan8 (= 14-20240330-1ubuntu2), libatomic1 (= 14-20240330-1ubuntu2), libattr1 (= 1:2.5.2-1build1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbinutils (= 2.42-4ubuntu2), libblas-dev (= 3.12.0-3build1), libblas3 (= 3.12.0-3build1), libblkid1 (= 2.39.3-9ubuntu6), libboost-dev (= 1.83.0.1ubuntu2), libboost-mpi-dev (= 1.83.0.1ubuntu2), libboost-mpi1.83-dev (= 1.83.0-2.1ubuntu3), libboost-mpi1.83.0 (= 1.83.0-2.1ubuntu3), libboost-serialization-dev (= 1.83.0.1ubuntu2), libboost-serialization1.83-dev (= 1.83.0-2.1ubuntu3), libboost-serialization1.83.0 (= 1.83.0-2.1ubuntu3), libboost1.83-dev (= 1.83.0-2.1ubuntu3), libbrotli1 (= 1.1.0-2build2), libbsd0 (= 0.12.1-1build1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8), libc-dev-bin (= 2.39-0ubuntu8), libc6 (= 2.39-0ubuntu8), libc6-dev (= 2.39-0ubuntu8), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu2), libcbor0.10 (= 0.10.2-1.2ubuntu2), libcc1-0 (= 14-20240330-1ubuntu2), libcom-err2 (= 1.47.0-2.4~exp1ubuntu4), libcrypt-dev (= 1:4.4.36-4build1), libcrypt1 (= 1:4.4.36-4build1), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcurl4t64 (= 8.5.0-2ubuntu10), libdb5.3t64 (= 5.3.28+dfsg2-6build1), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdpkg-perl (= 1.22.6ubuntu6), libdw1t64 (= 0.190-1.1build4), libedit2 (= 3.1-20230828-1build1), libelf1t64 (= 0.190-1.1build4), libevent-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-core-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-dev (= 2.1.12-stable-9ubuntu2), libevent-extra-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-openssl-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-9ubuntu2), libexpat1 (= 2.6.1-2build1), libfabric1 (= 1.17.0-3build2), libffi8 (= 3.4.6-1build1), libfido2-1 (= 1.14.0-1build2), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-23ubuntu3), libgcc-s1 (= 14-20240330-1ubuntu2), libgcrypt20 (= 1.10.3-2build1), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgfortran-13-dev (= 13.2.0-23ubuntu3), libgfortran5 (= 14-20240330-1ubuntu2), libgmp10 (= 2:6.3.0+dfsg-2ubuntu5), libgnutls30t64 (= 3.8.3-1.1ubuntu3), libgomp1 (= 14-20240330-1ubuntu2), libgpg-error0 (= 1.47-3build2), libgssapi-krb5-2 (= 1.20.1-6ubuntu2), libhogweed6t64 (= 3.9.1-2.2build1), libhwloc-dev (= 2.10.0-1), libhwloc-plugins (= 2.10.0-1), libhwloc15 (= 2.10.0-1), libibverbs-dev (= 50.0-2build2), libibverbs1 (= 50.0-2build2), libicu-dev (= 74.2-1ubuntu3), libicu74 (= 74.2-1ubuntu3), libidn2-0 (= 2.3.7-2build1), libisl23 (= 0.26-3build1), libjansson4 (= 2.14-2build2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjsoncpp25 (= 1.9.5-6build1), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3build1), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), liblapack-dev (= 3.12.0-3build1), liblapack3 (= 3.12.0-3build1), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu8), libltdl-dev (= 2.4.7-7build1), libltdl7 (= 2.4.7-7build1), liblz4-1 (= 1.9.4-1build1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmd0 (= 1.1.0-2build1), libmount1 (= 2.39.3-9ubuntu6), libmpc3 (= 1.3.1-1build1), libmpfr6 (= 4.2.1-1build1), libmunge2 (= 0.5.15-4build1), libncursesw6 (= 6.4+20240113-1ubuntu2), libnettle8t64 (= 3.9.1-2.2build1), libnghttp2-14 (= 1.59.0-1build2), libnl-3-200 (= 3.7.0-0.3build1), libnl-3-dev (= 3.7.0-0.3build1), libnl-route-3-200 (= 3.7.0-0.3build1), libnl-route-3-dev (= 3.7.0-0.3build1), libnuma-dev (= 2.0.18-1build1), libnuma1 (= 2.0.18-1build1), libopenmpi-dev (= 4.1.6-7ubuntu2), libopenmpi3t64 (= 4.1.6-7ubuntu2), libp11-kit0 (= 0.25.3-4ubuntu2), libpam-modules (= 1.5.3-5ubuntu4), libpam-modules-bin (= 1.5.3-5ubuntu4), libpam-runtime (= 1.5.3-5ubuntu4), libpam0g (= 1.5.3-5ubuntu4), libpciaccess0 (= 0.17-3build1), libpcre2-8-0 (= 10.42-4ubuntu2), libperl5.38t64 (= 5.38.2-3.2build2), libpipeline1 (= 1.5.7-2), libpmix-dev (= 5.0.1-4.1build1), libpmix2t64 (= 5.0.1-4.1build1), libproc2-0 (= 2:4.0.4-4ubuntu3), libpsl5t64 (= 0.21.2-1.1build1), librdmacm1t64 (= 50.0-2build2), librhash0 (= 1.4.3-3build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build7), libsasl2-2 (= 2.1.28+dfsg1-5ubuntu3), libsasl2-modules-db (= 2.1.28+dfsg1-5ubuntu3), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libsemanage-common (= 3.5-1build5), libsemanage2 (= 3.5-1build5), libsepol2 (= 3.5-2build1), libsframe1 (= 2.42-4ubuntu2), libsmartcols1 (= 2.39.3-9ubuntu6), libssh-4 (= 0.10.6-2build2), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu3), libstdc++6 (= 14-20240330-1ubuntu2), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu7), libtasn1-6 (= 4.19.0-3build1), libtinfo6 (= 6.4+20240113-1ubuntu2), libtool (= 2.4.7-7build1), libubsan1 (= 14-20240330-1ubuntu2), libuchardet0 (= 0.0.8-1build1), libudev1 (= 255.4-1ubuntu7), libunistring5 (= 1.1-2build1), libuuid1 (= 2.39.3-9ubuntu6), libuv1t64 (= 1.48.0-1.1build1), libx11-6 (= 2:1.8.7-1build1), libx11-data (= 2:1.8.7-1build1), libxau6 (= 1:1.0.9-1build6), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu6), libxext6 (= 2:1.3.4-1build2), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libxml2-dev (= 2.9.14+dfsg-1.3ubuntu3), libxnvctrl0 (= 510.47.03-0ubuntu4), libzstd1 (= 1.5.5+dfsg2-2build1), linux-libc-dev (= 6.8.0-22.22), login (= 1:4.13+dfsg1-4ubuntu3), lto-disabled-list (= 47), m4 (= 1.4.19-4build1), make (= 4.3-4.1build2), man-db (= 2.12.0-4build2), mawk (= 1.3.4.20240123-1build1), mpi-default-dev (= 1.15), ncurses-base (= 6.4+20240113-1ubuntu2), ncurses-bin (= 6.4+20240113-1ubuntu2), ocl-icd-libopencl1 (= 2.3.2-1), openmpi-bin (= 4.1.6-7ubuntu2), openmpi-common (= 4.1.6-7ubuntu2), openssh-client (= 1:9.6p1-3ubuntu13), passwd (= 1:4.13+dfsg1-4ubuntu3), patch (= 2.7.6-7build3), perl (= 5.38.2-3.2build2), perl-base (= 5.38.2-3.2build2), perl-modules-5.38 (= 5.38.2-3.2build2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-4ubuntu3), rpcsvc-proto (= 1.4.2-0ubuntu7), sed (= 4.9-2build1), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu3), tar (= 1.35+dfsg-3build1), util-linux (= 2.39.3-9ubuntu6), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1712873628" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ prime-phylo_1.0.11-10ubuntu1_armhf.deb -------------------------------------- new Debian package, version 2.0. size 804298 bytes: control archive=1758 bytes. 1178 bytes, 20 lines control 2025 bytes, 31 lines md5sums Package: prime-phylo Version: 1.0.11-10ubuntu1 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 2015 Depends: perl:any, libblas3 | libblas.so.3, libboost-mpi1.83.0 (>= 1.83.0), libboost-serialization1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.5), liblapack3 | liblapack.so.3, libopenmpi3t64 (>= 4.1.6), libstdc++6 (>= 13.1), libxml2 (>= 2.7.4) Suggests: njplot, treeviewx, muscle, probalign, mafft, python3-biopython, mrbayes, phyml, raxml Section: science Priority: optional Homepage: http://prime.sbc.su.se Description: bayesian estimation of gene trees taking the species tree into account PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. . The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-04-11 22:13 ./ drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/ drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/bin/ -rwxr-xr-x root/root 26392 2024-04-11 22:13 ./usr/bin/chainsaw -rwxr-xr-x root/root 33128 2012-12-17 15:52 ./usr/bin/mcmc_analysis -rwxr-xr-x root/root 75416 2024-04-11 22:13 ./usr/bin/primeDLRS -rwxr-xr-x root/root 79512 2024-04-11 22:13 ./usr/bin/primeDTLSR -rwxr-xr-x root/root 34880 2024-04-11 22:13 ./usr/bin/primeGEM lrwxrwxrwx root/root 0 2024-04-11 22:13 ./usr/bin/primeGSRf -> primeDLRS -rwxr-xr-x root/root 34532 2024-04-11 22:13 ./usr/bin/reconcile -rwxr-xr-x root/root 38792 2024-04-11 22:13 ./usr/bin/reroot -rwxr-xr-x root/root 22432 2024-04-11 22:13 ./usr/bin/showtree -rwxr-xr-x root/root 18124 2024-04-11 22:13 ./usr/bin/tree2leafnames -rwxr-xr-x root/root 18144 2024-04-11 22:13 ./usr/bin/treesize drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/lib/ drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/lib/prime-phylo/ -rw-r--r-- root/root 34352 2024-04-11 22:13 ./usr/lib/prime-phylo/libprime-phylo-sfile.so -rw-r--r-- root/root 1595020 2024-04-11 22:13 ./usr/lib/prime-phylo/libprime-phylo.so drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/share/ drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/share/doc/prime-phylo/ -rw-r--r-- root/root 381 2012-12-17 15:52 ./usr/share/doc/prime-phylo/README -rw-r--r-- root/root 532 2024-04-11 22:09 ./usr/share/doc/prime-phylo/README.test -rw-r--r-- root/root 869 2024-04-11 22:13 ./usr/share/doc/prime-phylo/changelog.Debian.gz -rw-r--r-- root/root 7287 2024-04-11 22:09 ./usr/share/doc/prime-phylo/copyright drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/share/doc/prime-phylo/examples/ -rw-r--r-- root/root 393 2024-04-11 22:09 ./usr/share/doc/prime-phylo/examples/gse -rw-r--r-- root/root 162 2024-04-11 22:09 ./usr/share/doc/prime-phylo/examples/hostfile -rw-r--r-- root/root 3513 2024-04-11 22:09 ./usr/share/doc/prime-phylo/examples/seqfile -rw-r--r-- root/root 14 2024-04-11 22:09 ./usr/share/doc/prime-phylo/examples/treefile -rw-r--r-- root/root 974 2024-04-11 22:09 ./usr/share/doc/prime-phylo/run-unit-test drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/share/man/ drwxr-xr-x root/root 0 2024-04-11 22:13 ./usr/share/man/man1/ -rw-r--r-- root/root 653 2024-04-11 22:13 ./usr/share/man/man1/chainsaw.1.gz -rw-r--r-- root/root 1284 2024-04-11 22:13 ./usr/share/man/man1/mcmc_analysis.1.gz -rw-r--r-- root/root 2154 2024-04-11 22:13 ./usr/share/man/man1/primeDLRS.1.gz -rw-r--r-- root/root 1992 2024-04-11 22:13 ./usr/share/man/man1/primeDTLSR.1.gz -rw-r--r-- root/root 987 2024-04-11 22:13 ./usr/share/man/man1/primeGEM.1.gz lrwxrwxrwx root/root 0 2024-04-11 22:13 ./usr/share/man/man1/primeGSRf.1.gz -> primeDLRS.1.gz -rw-r--r-- root/root 654 2024-04-11 22:13 ./usr/share/man/man1/reconcile.1.gz -rw-r--r-- root/root 886 2024-04-11 22:13 ./usr/share/man/man1/reroot.1.gz -rw-r--r-- root/root 904 2024-04-11 22:13 ./usr/share/man/man1/showtree.1.gz -rw-r--r-- root/root 494 2024-04-11 22:13 ./usr/share/man/man1/tree2leafnames.1.gz -rw-r--r-- root/root 608 2024-04-11 22:13 ./usr/share/man/man1/treesize.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 107476 Build-Time: 651 Distribution: noble Host Architecture: armhf Install-Time: 78 Job: prime-phylo_1.0.11-10ubuntu1.dsc Machine Architecture: arm64 Package: prime-phylo Package-Time: 733 Source-Version: 1.0.11-10ubuntu1 Space: 107476 Status: successful Version: 1.0.11-10ubuntu1 -------------------------------------------------------------------------------- Finished at 2024-04-11T22:30:49Z Build needed 00:12:13, 107476k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-28050319 Scanning for processes to kill in build PACKAGEBUILD-28050319