Diff of the two buildlogs: -- --- b1/build.log 2023-05-08 22:40:51.552950924 +0000 +++ b2/build.log 2023-05-08 23:14:49.403754633 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 8 10:06:48 -12 2023 -I: pbuilder-time-stamp: 1683583608 +I: Current time: Tue May 9 12:41:29 +14 2023 +I: pbuilder-time-stamp: 1683585689 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./prime-phylo_1.0.11.orig.tar.gz] I: copying [./prime-phylo_1.0.11-10.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Aug 15 02:21:26 2021 -12 +gpgv: Signature made Mon Aug 16 04:21:26 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -31,135 +31,167 @@ dpkg-source: info: applying 0004-fix-gcc10-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/31272/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/D01_modify_environment starting +debug: Running on ff4a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 9 12:42 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='2239b08892c640b3974838a96de0afe5' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='31272' - PS1='# ' - PS2='> ' + INVOCATION_ID=1ec67595f22e4bc6abcf5d5262d092fd + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=30966 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TM0hAjIU/pbuilderrc_Xsdd --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TM0hAjIU/b1 --logfile b1/build.log prime-phylo_1.0.11-10.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TM0hAjIU/pbuilderrc_Co71 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TM0hAjIU/b2 --logfile b2/build.log --extrapackages usrmerge prime-phylo_1.0.11-10.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64a 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/31272/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 9 12:42 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -338,7 +370,7 @@ Get: 115 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 116 http://deb.debian.org/debian bookworm/main armhf liblapack-dev armhf 3.11.0-2 [1798 kB] Get: 117 http://deb.debian.org/debian bookworm/main armhf libxml2-dev armhf 2.9.14+dfsg-1.2 [709 kB] -Fetched 73.8 MB in 1min 36s (769 kB/s) +Fetched 73.8 MB in 10s (7510 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) @@ -830,8 +862,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/prime-phylo-1.0.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../prime-phylo_1.0.11-10_source.changes +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/prime-phylo-1.0.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../prime-phylo_1.0.11-10_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-10 dpkg-buildpackage: info: source distribution unstable @@ -990,7 +1033,7 @@ -- Build files have been written to: /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/prime-phylo-1.0.11' dh_auto_build -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/prime-phylo-1.0.11 -B/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/CMakeFiles /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -1013,9 +1056,11 @@ make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' [ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/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/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gbread.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c -[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o +[ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/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/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c +[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/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/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -MF CMakeFiles/prime-phylo-sfile.dir/lexer.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/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/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -MF CMakeFiles/prime-phylo-sfile.dir/sfile.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c: In function 'main': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] @@ -1025,6 +1070,14 @@ 7 | #include "gb.tab.h" +++ |+#include 8 | +/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c: In function 'yyparse': +/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c:1096:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration] + 1096 | yychar = yylex (); + | ^~~~~ +gb.y: In function 'yyerror': +gb.y:291:70: warning: implicit declaration of function 'linenumber' [-Wimplicit-function-declaration] +gb.y: In function 'add_to_seq': +gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable] /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_print': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:265:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] 265 | printf("%9d", char_counter + 1); @@ -1034,8 +1087,6 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable 'date' set but not used [-Wunused-but-set-variable] 212 | char *top, *date; | ^~~~ -[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/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/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c seqreader.l: In function 'seq_read': seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable] /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c: At top level: @@ -1045,14 +1096,6 @@ /build/prime-phylo-1.0.11/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 ) | ^~~~~~~ -/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c: In function 'yyparse': -/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c:1096:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration] - 1096 | yychar = yylex (); - | ^~~~~ -gb.y: In function 'yyerror': -gb.y:291:70: warning: implicit declaration of function 'linenumber' [-Wimplicit-function-declaration] -gb.y: In function 'add_to_seq': -gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable] /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_add_comment': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:303:20: warning: array subscript 'struct comment[0]' is partly outside array bounds of 'unsigned char[4]' [-Warray-bounds] 303 | tmp->text = strdup(s); @@ -1085,11 +1128,13 @@ make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -MF CMakeFiles/prime-phylo.dir/NHXtree.c.o.d -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -MF CMakeFiles/prime-phylo.dir/NHXannotation.c.o.d -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c +[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -MF CMakeFiles/prime-phylo.dir/NHXtree.c.o.d -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c:155:32: warning: format '%d' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=] 155 | fprintf(stderr, "BW:\t%d\n", l->arg.t); @@ -1097,20 +1142,18 @@ | | | | int double | %f -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function 'new_annotation': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c:80:3: warning: '__builtin_strncpy' specified bound 5 equals destination size [-Wstringop-truncation] - 80 | strncpy(a->anno_type, tag, MAX_ANNOTATION_ID_LENGTH); - | ^ -[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c -[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -MF CMakeFiles/prime-phylo.dir/NHXparse.c.o.d -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c /build/prime-phylo-1.0.11/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) | ^~~~~ /build/prime-phylo-1.0.11/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 ) | ^~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function 'new_annotation': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c:80:3: warning: '__builtin_strncpy' specified bound 5 equals destination size [-Wstringop-truncation] + 80 | strncpy(a->anno_type, tag, MAX_ANNOTATION_ID_LENGTH); + | ^ +[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -MF CMakeFiles/prime-phylo.dir/NHXparse.c.o.d -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c [ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -MF CMakeFiles/prime-phylo.dir/AnError.cc.o.d -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c: In function 'yytree_parse': @@ -1139,6 +1182,8 @@ cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o -MF CMakeFiles/prime-phylo.dir/ODESolver.cc.o.d -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc [ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o -MF CMakeFiles/prime-phylo.dir/PRNG.cc.o.d -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.cc +[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -MF CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o.d -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc:4: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; @@ -1248,10 +1293,18 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ -[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -MF CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o.d -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] + 405 | catch(std::exception e) + | ^ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] + 423 | catch(std::exception e) + | ^ [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -MF CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc +[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -MF CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.hh:10, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:5: @@ -1270,58 +1323,48 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] - 405 | catch(std::exception e) - | ^ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] - 423 | catch(std::exception e) - | ^ +[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -MF CMakeFiles/prime-phylo.dir/Probability.cc.o.d -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc +In file included from /usr/include/c++/12/vector:70, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.hh:12, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:1: +/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:624:13: + inlined from 'void beep::TmplPrimeOption::parseParams(std::string&, unsigned int, std::vector&) [with T = double]' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:286:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -MF CMakeFiles/prime-phylo.dir/Tokenizer.cc.o.d -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:625:13: + inlined from 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:400:16: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:626:13: + inlined from 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:415:16: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -MF CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc -In file included from /usr/include/c++/12/vector:70, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.hh:12, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:1: -/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:286:22: + inlined from 'std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:624:13: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -MF CMakeFiles/prime-phylo.dir/Probability.cc.o.d -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:400:16: + inlined from 'std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:625:13: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:415:16: + inlined from 'std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:626:13: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -MF CMakeFiles/prime-phylo.dir/Tokenizer.cc.o.d -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -MF CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o.d -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TimeEstimator.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o @@ -1332,6 +1375,8 @@ cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscTree.cc +[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator @@ -1376,8 +1421,43 @@ /usr/include/c++/12/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/EpochPtMaps.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc +[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc +In file included from /usr/include/c++/12/vector:70, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.hh:6, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:5: +/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/12/vector:64: +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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:22:19: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _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++/12/bits/stl_vector.h:1294:21, + inlined from 'beep::EpochPtSet::EpochPtSet(std::vector, beep::Real, beep::Real, unsigned int)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:25:20: +/usr/include/c++/12/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:27:19: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o -MF CMakeFiles/prime-phylo.dir/EpochTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] + 54 | static const Real MIN_SPLICE_DELTA = 0.0001; + | ^~~~~~~~~~~~~~~~ +[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -MF CMakeFiles/prime-phylo.dir/InvMRCA.cc.o.d -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvMRCA.cc In file included from /usr/include/c++/12/vector:63, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:4: @@ -1394,13 +1474,6 @@ /usr/include/c++/12/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] - 54 | static const Real MIN_SPLICE_DELTA = 0.0001; - | ^~~~~~~~~~~~~~~~ -[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.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++/12/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++/12/bits/stl_uninitialized.h:372:37, @@ -1500,34 +1573,6 @@ /usr/include/c++/12/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); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o -MF CMakeFiles/prime-phylo.dir/EpochTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc -In file included from /usr/include/c++/12/vector:70, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.hh:6, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:5: -/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:64: -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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:22:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _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++/12/bits/stl_vector.h:1294:21, - inlined from 'beep::EpochPtSet::EpochPtSet(std::vector, beep::Real, beep::Real, unsigned int)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:25:20: -/usr/include/c++/12/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtSet.cc:27:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:7: /usr/include/c++/12/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]': @@ -1535,8 +1580,6 @@ 309 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc:309:7: 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 /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -MF CMakeFiles/prime-phylo.dir/InvMRCA.cc.o.d -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvMRCA.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap::set(unsigned int, unsigned int, const_iterator) [with T = double]': /build/prime-phylo-1.0.11/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) @@ -1610,6 +1653,12 @@ /build/prime-phylo-1.0.11/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, | ^~~~~~~~~~ +[ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o -MF CMakeFiles/prime-phylo.dir/Node.cc.o.d -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Node.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] + 54 | static const Real MIN_SPLICE_DELTA = 0.0001; + | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; = void; _Tp = beep::Probability; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:823:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 823 | assign(_InputIterator __first, _InputIterator __last) @@ -1643,12 +1692,6 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:422:25: note: parameter passing for argument of type 'beep::EpochPtPtMap::const_iterator' {aka 'std::vector >::const_iterator'} changed in GCC 7.1 422 | v.assign(start, start + v.size()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] - 54 | static const Real MIN_SPLICE_DELTA = 0.0001; - | ^~~~~~~~~~~~~~~~ -[ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o -MF CMakeFiles/prime-phylo.dir/Node.cc.o.d -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Node.cc In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:7: /usr/include/c++/12/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]': @@ -1681,6 +1724,10 @@ cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -MF CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc [ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizer.cc +[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizers.cc +[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizer.hh:6, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizer.cc:6: @@ -1714,34 +1761,6 @@ 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:7: -/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -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 /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:517:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _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 /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:521:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _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 /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:525:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizers.cc -In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizers.hh:6, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizers.cc:4: /usr/include/c++/12/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]': @@ -1768,6 +1787,13 @@ /usr/include/c++/12/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++/12/vector:70, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:7: +/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizers.cc:54:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 @@ -1785,12 +1811,31 @@ /usr/include/c++/12/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/TreeMCMC.cc.o [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc [ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -MF CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc +In file included from /usr/include/c++/12/vector:64: +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 /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:517:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _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 /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:521:21: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _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 /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc:525:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc: In constructor 'beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const beep::Real&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:26:15: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] 26 | old_times(NULL), @@ -1813,10 +1858,14 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ +[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -MF CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o.d -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:118:29: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] 118 | buf[ bytes_read ]=NULL; | ^~~~ +[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc In file included from /usr/include/c++/12/vector:63, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator > >; _ForwardIterator = beep::Probability*]': @@ -1852,6 +1901,8 @@ /usr/include/c++/12/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 /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_common.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector*, beep::StrStrMap*, std::map*, std::map*)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:29: warning: 'idInt' may be used uninitialized [-Wmaybe-uninitialized] 1049 | new_node = S.addNode(l, r, idInt, name); @@ -1859,6 +1910,8 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:959:9: note: 'idInt' was declared here 959 | int idInt; | ^~~~~ +[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:10, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc:1: @@ -1866,20 +1919,26 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] + 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ + | ^~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:6: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] + 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ In file included from /usr/include/c++/12/vector:64: 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc:274:14: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -MF CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o.d -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc -[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc -[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_common.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc +[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.cc +[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC.cc +[ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.hh:13, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1: @@ -1893,22 +1952,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] - 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ - | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:6: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] - 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ -[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.cc -[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC.cc -[ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc +[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function 'void beep::EdgeRateMCMC_common::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable 'fparam' [-Wunused-variable] 104 | Real fparam = std::log(rate) - 0.5 * variance * (rtime - 3.0 * ltime); @@ -1916,20 +1961,18 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable 'rparam' [-Wunused-variable] 105 | Real rparam = variance * (rtime + ltime); | ^~~~~~ -[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 106 | for (int i = 0; i < t.size(); i++) - | ~~^~~~~~~~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -MF CMakeFiles/prime-phylo.dir/GammaDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -MF CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 106 | for (int i = 0; i < t.size(); i++) + | ~~^~~~~~~~~~ [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: @@ -1940,12 +1983,12 @@ cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -MF CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -MF CMakeFiles/prime-phylo.dir/NormalDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc -[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -MF CMakeFiles/prime-phylo.dir/UniformDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ +[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -MF CMakeFiles/prime-phylo.dir/UniformDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. @@ -1956,18 +1999,20 @@ cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -MF CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc +[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ -[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCModel.cc [ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCObject.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCObject.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc +[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. @@ -1976,8 +2021,6 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ -[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc: In member function 'virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable 'check_number_nonupdate' set but not used [-Wunused-but-set-variable] 78 | unsigned check_number_nonupdate = 0; @@ -2006,6 +2049,10 @@ | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:27: warning: operation on 'i' may be undefined [-Wsequence-point] /build/prime-phylo-1.0.11/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 /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc +[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.cc In file included from /usr/include/c++/12/map:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.hh:14, @@ -2062,8 +2109,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc +[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc In file included from /usr/include/c++/12/vector:63, from /usr/include/c++/12/functional:62, from /usr/include/boost/utility/compare_pointees.hpp:15, @@ -2099,17 +2146,16 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc +[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc 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++/12/bits/stl_vector.h:1294:21, inlined from 'void beep::MpiMultiGSR::updateGvars(unsigned int)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:223:17: /usr/include/c++/12/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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.cc -[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc -[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o In file included from /usr/include/c++/12/vector:63, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, @@ -2119,7 +2165,6 @@ 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.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++/12/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++/12/bits/stl_uninitialized.h:372:37, @@ -2155,10 +2200,12 @@ /usr/include/c++/12/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); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc +[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc +[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, @@ -2242,8 +2289,6 @@ /usr/include/c++/12/bits/stl_vector.h:1737:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1737 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator @@ -2276,8 +2321,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -MF CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, @@ -2454,6 +2497,8 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ +[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -MF CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ @@ -2580,16 +2625,6 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ -[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -MF CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc -In file included from /usr/include/c++/12/vector:70, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:6: -/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] @@ -2700,16 +2735,22 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ +[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o -MF CMakeFiles/prime-phylo.dir/GammaMap.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc +In file included from /usr/include/c++/12/vector:70, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:6: +/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:239:10: /usr/include/c++/12/bits/stl_vector.h:1435:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1435 | _M_fill_insert(begin() + __offset, __n, __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o -MF CMakeFiles/prime-phylo.dir/GammaMap.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc -[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; @@ -2720,8 +2761,12 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ +[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc +[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc In file included from /usr/include/c++/12/vector:63, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, @@ -2773,27 +2818,12 @@ /usr/include/c++/12/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); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc [ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -MF CMakeFiles/prime-phylo.dir/LambdaMap.cc.o.d -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.cc -In file included from /usr/include/c++/12/vector:70, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:5, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: -/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | 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++/12/bits/stl_vector.h:1294:21, - inlined from 'beep::fastGEM_BirthDeathProbs::fastGEM_BirthDeathProbs(beep::Tree&, unsigned int, std::vector >*, const beep::Real&, const beep::Real&)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:30:24: -/usr/include/c++/12/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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)': @@ -2812,6 +2842,19 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1356:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable] 1356 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:5, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: +/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | 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++/12/bits/stl_vector.h:1294:21, + inlined from 'beep::fastGEM_BirthDeathProbs::fastGEM_BirthDeathProbs(beep::Tree&, unsigned int, std::vector >*, const beep::Real&, const beep::Real&)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:30:24: +/usr/include/c++/12/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 /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -MF CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o.d -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o @@ -2822,20 +2865,26 @@ cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc -[ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ +[ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc +[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] 161 | Probability p = calculateDataProbability(); | ^ -[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc +[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::string beep::ReconciliationTimeModel::table4os() const': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] + 319 | typedef std::map::const_iterator MapIter; + | ^~~~~~~ In file included from /usr/include/c++/12/vector:63, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, @@ -2875,28 +2924,26 @@ /usr/include/c++/12/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/ReconciliationTimeSampler.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::string beep::ReconciliationTimeModel::table4os() const': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] - 319 | typedef std::map::const_iterator MapIter; - | ^~~~~~~ [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -MF CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o.d -o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc +[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -MF CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o.d -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function 'const std::string beep::ReconciliationTimeSampler::table4os() const': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] 422 | typedef std::map::const_iterator MapIter; | ^~~~~~~ -[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -MF CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o.d -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc +[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc +[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const std::string&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: 'beep::ReconciliationTreeGenerator::R' is initialized with itself [-Winit-self] 31 | ReconciliationTreeGenerator:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc +[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTree.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:22, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: @@ -2934,18 +2981,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc -[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTree.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc +[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc +[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:367:40: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] + 367 | if(rootNode && bTree.getRootNode() == false) + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/c++/12/map:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:13: /usr/include/c++/12/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++/12/bits/stl_tree.h:2457:7: 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 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc In file included from /usr/include/c++/12/map:61: 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++/12/bits/stl_map.h:858:27, @@ -2955,46 +3004,44 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 639 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:367:40: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] - 367 | if(rootNode && bTree.getRootNode() == false) - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc In file included from /usr/include/c++/12/vector:70, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.hh:13, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.hh:4, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:1: + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:10, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:1: /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:130:14: + inlined from 'std::vector beep::HybridTreeIO::readAllHybridTrees(beep::TreeIOTraits, std::vector*, std::vector*)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:236:14: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc In file included from /usr/include/c++/12/vector:70, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:10, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:1: + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.hh:13, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.hh:4, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:1: /usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc In file included from /usr/include/c++/12/vector:64: 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:236:14: + inlined from 'std::vector beep::HybridTreeInputOutput::readAllHybridTrees(beep::TreeIOTraits&, std::vector*, std::vector*)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:130:14: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc -[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc +[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc +[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc In file included from /usr/include/c++/12/map:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.hh:4, @@ -3077,12 +3124,32 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc -[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc +[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc +[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc +[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] + 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/utility/compare_pointees.hpp:15, + from /usr/include/boost/optional/optional.hpp:55, + from /usr/include/boost/optional.hpp:15, + from /usr/include/boost/mpi/environment.hpp:18, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.hh:4, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.hh:7, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.hh:4, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:1: +/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:63, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, @@ -3092,8 +3159,6 @@ 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 -[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.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++/12/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++/12/bits/stl_uninitialized.h:372:37, @@ -3124,37 +3189,8 @@ /usr/include/c++/12/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++/12/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++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'beep::NodeNodeMap::NodeNodeMap(const beep::NodeNodeMap&) [with T = beep::Probability]' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.hh:28:2, - inlined from 'beep::HybridGuestTreeModel::HybridGuestTreeModel(const beep::HybridGuestTreeModel&)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:60:7: -/usr/include/c++/12/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); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc -[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] - 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/utility/compare_pointees.hpp:15, - from /usr/include/boost/optional/optional.hpp:55, - from /usr/include/boost/optional.hpp:15, - from /usr/include/boost/mpi/environment.hpp:18, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.hh:4, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.hh:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.hh:4, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:1: -/usr/include/c++/12/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++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc In file included from /usr/include/c++/12/vector:64: 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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:251:16: @@ -3176,8 +3212,15 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.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++/12/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++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = beep::Probability; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'beep::NodeNodeMap::NodeNodeMap(const beep::NodeNodeMap&) [with T = beep::Probability]' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.hh:28:2, + inlined from 'beep::HybridGuestTreeModel::HybridGuestTreeModel(const beep::HybridGuestTreeModel&)' at /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:60:7: +/usr/include/c++/12/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 /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o @@ -3188,11 +3231,15 @@ /usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: +[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixCache.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.cc +[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ @@ -3265,16 +3312,19 @@ /usr/include/c++/12/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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixCache.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.cc -[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o -MF CMakeFiles/prime-phylo.dir/SeqIO.cc.o.d -o CMakeFiles/prime-phylo.dir/SeqIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SeqIO.cc [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc +[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceType.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + | ^~~ In file included from /usr/include/c++/12/map:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.hh:5, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc:7: @@ -3355,15 +3405,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceType.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ -[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceData.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc In file included from /usr/include/c++/12/vector:63, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:4: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = beep::MatrixTransitionHandler*]': @@ -3395,8 +3436,16 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a 'friend' 56 | friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); | ^~~~~~~~ +[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceData.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc +[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map beep::SequenceData::getBaseFrequencies()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 288 | for (int i = 0; i < seqType.alphabetSize(); i++) @@ -3404,12 +3453,20 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:303:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wsign-compare] 303 | for (int j = 0; j < seq.length(); j++) { | ~~^~~~~~~~~~~~~~ -[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ +[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Vector.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc +[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc +[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -MF CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:19:5: warning: 'beep::LA_Matrix::dim' is initialized with itself [-Winit-self] + 19 | LA_Matrix::LA_Matrix() + | ^~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:20:13: warning: '*this.beep::LA_Matrix::dim' is used uninitialized [-Wuninitialized] + 20 | : dim(dim), + | ^~~ In file included from /usr/include/c++/12/vector:70, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:6: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': @@ -3561,20 +3618,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Vector.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc -[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:19:5: warning: 'beep::LA_Matrix::dim' is initialized with itself [-Winit-self] - 19 | LA_Matrix::LA_Matrix() - | ^~~~~~~~~ -[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 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/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.1.74.0 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so.1.74.0 ../sfile/libprime-phylo-sfile.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so @@ -3583,29 +3626,63 @@ make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend +make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build [ 82%] Generating cmdline.c, cmdline.h -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build -[ 82%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build +[ 83%] Generating cmdline.c, cmdline.h +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +[ 83%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o +[ 83%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -MF CMakeFiles/primeDLRS.dir/primeDLRS.cc.o.d -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= -[ 82%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -MF CMakeFiles/primeDTLSR.dir/idolatrous.cc.o.d -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o +[ 83%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o -MF CMakeFiles/primeGEM.dir/troyo.cc.o.d -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc +[ 83%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o -MF CMakeFiles/treesize.dir/treesize.cc.o.d -o CMakeFiles/treesize.dir/treesize.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc +/build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc: In function 'int main(int, char**)': +/build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:55:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] + 55 | switch(args_info.input_format_arg) + | ^ +/build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:90:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 90 | catch (AnError e) { + | ^ +[ 84%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o -MF CMakeFiles/treesize.dir/cmdline.c.o.d -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c +[ 85%] Linking CXX executable treesize +cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so +make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +[ 85%] Generating cmdline.c, cmdline.h +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +[ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o -MF CMakeFiles/showtree.dir/showtree.cc.o.d -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -3654,6 +3731,10 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)': +/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:30:20: warning: variable 'nw' set but not used [-Wunused-but-set-variable] + 30 | bool et, nt, bl, nw; + | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: @@ -3771,6 +3852,13 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'int main(int, char**)': +/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:174:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] + 174 | if(args_info.tree_number_arg >= Tvec.size()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:198:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 198 | catch (AnError e) + | ^ In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:16: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ @@ -3791,6 +3879,8 @@ /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:25: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 197 | catch(AnError e) | ^ +[ 86%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o -MF CMakeFiles/showtree.dir/cmdline.c.o.d -o CMakeFiles/showtree.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.c /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/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"); @@ -3799,130 +3889,69 @@ /build/prime-phylo-1.0.11/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"); | ^ -[ 83%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -MF CMakeFiles/primeGEM.dir/cmdline.c.o.d -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.c -[ 83%] Linking CXX executable primeGEM -cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 83%] Built target primeGEM -make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 84%] Generating cmdline.c, cmdline.h -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 84%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE 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main(int, char**)': -/build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:55:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] - 55 | switch(args_info.input_format_arg) - | ^ -/build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:90:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 90 | catch (AnError e) { - | ^ -[ 85%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o -MF CMakeFiles/treesize.dir/cmdline.c.o.d -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c -[ 86%] Linking CXX executable treesize -cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 86%] Built target treesize -make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 86%] Generating cmdline.c, cmdline.h -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -[ 87%] Linking CXX executable primeDLRS -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1 -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree 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'/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 88%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o -MF CMakeFiles/showtree.dir/showtree.cc.o.d -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc +[ 87%] Linking CXX executable showtree +cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 88%] Built target primeDLRS +[ 87%] Built target showtree make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 89%] Generating cmdline.c, cmdline.h +[ 88%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 90%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o +[ 89%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o -MF CMakeFiles/reconcile.dir/Rootalyzer.cc.o.d -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc -[ 91%] Linking CXX executable primeDTLSR -cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/build/prime-phylo-1.0.11/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.1.74.0 /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.1.74.0 +[ 90%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -MF CMakeFiles/primeGEM.dir/cmdline.c.o.d -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.c +[ 90%] Linking CXX executable primeGEM +cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 91%] Built target primeDTLSR +[ 90%] Built target primeGEM make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 92%] Generating cmdline.c, cmdline.h +[ 91%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 92%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o +[ 91%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o -MF CMakeFiles/reroot.dir/reroot.cc.o.d -o CMakeFiles/reroot.dir/reroot.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc -/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)': -/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:30:20: warning: variable 'nw' set but not used [-Wunused-but-set-variable] - 30 | bool et, nt, bl, nw; - | ^~ -/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'int main(int, char**)': -/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:174:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] - 174 | if(args_info.tree_number_arg >= Tvec.size()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:198:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 198 | catch (AnError e) - | ^ -[ 92%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o -MF CMakeFiles/showtree.dir/cmdline.c.o.d -o CMakeFiles/showtree.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.c -[ 93%] Linking CXX executable showtree -cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so +[ 92%] Linking CXX executable primeDLRS +cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/build/prime-phylo-1.0.11/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.1.74.0 /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.1.74.0 make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 93%] Built target showtree +[ 92%] Built target primeDLRS make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 93%] Generating cmdline.c, cmdline.h +[ 92%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 94%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o +[ 93%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -MF CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o.d -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc -/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)': -/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] - 51 | switch(args_info.input_format_arg) - | ^ -/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:95:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 95 | catch (AnError e) { - | ^ -[ 95%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -MF CMakeFiles/tree2leafnames.dir/cmdline.c.o.d -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c -[ 95%] Linking CXX executable tree2leafnames -cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so -[ 95%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o +[ 94%] Linking CXX executable primeDTLSR +cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/build/prime-phylo-1.0.11/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.1.74.0 /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.1.74.0 +[ 94%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -MF CMakeFiles/reconcile.dir/reconcile.cc.o.d -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 95%] Built target tree2leafnames +[ 94%] Built target primeDTLSR make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 95%] Generating cmdline.c, cmdline.h +[ 94%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/prime-phylo-1.0.11/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 '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o +[ 95%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o -MF CMakeFiles/chainsaw.dir/chainsaw.cc.o.d -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] @@ -3931,19 +3960,29 @@ /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:181:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 181 | catch (AnError e) { | ^ -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 37 | char *ofilename = "mpr.out"; - | ^~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 128 | catch (AnError e) { +/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)': +/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] + 51 | switch(args_info.input_format_arg) + | ^ +/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:95:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 95 | catch (AnError e) { | ^ -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 157 | for (int i = 0; i < gtree.getNumberOfNodes(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o +[ 96%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -MF CMakeFiles/tree2leafnames.dir/cmdline.c.o.d -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c +[ 96%] Linking CXX executable tree2leafnames +cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +[ 96%] Built target tree2leafnames +[ 96%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o -MF CMakeFiles/chainsaw.dir/cmdline.c.o.d -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c +[ 97%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o -MF CMakeFiles/reconcile.dir/cmdline.c.o.d -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.c +[ 98%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o -MF CMakeFiles/reroot.dir/cmdline.c.o.d -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.c +[ 99%] Linking CXX executable reroot +cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)': /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value 'guest_tree_format__NULL' not handled in switch [-Wswitch] 90 | switch(ai.guest_tree_format_arg) @@ -3959,15 +3998,19 @@ /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:188:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 188 | catch (AnError e) { | ^ -[ 98%] Linking CXX executable reroot -cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 98%] Built target reroot -[ 98%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o -MF CMakeFiles/chainsaw.dir/cmdline.c.o.d -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c -[ 99%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o -MF CMakeFiles/reconcile.dir/cmdline.c.o.d -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.c +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 37 | char *ofilename = "mpr.out"; + | ^~~~~~~~~ +[ 99%] Built target reroot +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 128 | catch (AnError e) { + | ^ +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 157 | for (int i = 0; i < gtree.getNumberOfNodes(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable chainsaw cd /build/prime-phylo-1.0.11/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=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so @@ -3986,7 +4029,7 @@ dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install --destdir=debian/prime-phylo/ -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/prime-phylo-1.0.11/debian/prime-phylo AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/prime-phylo-1.0.11/debian/prime-phylo AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/prime-phylo-1.0.11 -B/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -4050,18 +4093,18 @@ dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' -dpkg-shlibdeps: warning: 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/tree2leafnames 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: debian/prime-phylo/usr/bin/primeDLRS 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/showtree 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/treesize 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/chainsaw 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/reroot 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/tree2leafnames 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/primeGEM 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/treesize 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/chainsaw 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/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/showtree contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake @@ -4075,12 +4118,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30966/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/31272 and its subdirectories -I: Current time: Mon May 8 10:40:42 -12 2023 -I: pbuilder-time-stamp: 1683585642 +I: removing directory /srv/workspace/pbuilder/30966 and its subdirectories +I: Current time: Tue May 9 13:14:43 +14 2023 +I: pbuilder-time-stamp: 1683587683