Diff of the two buildlogs: -- --- b1/build.log 2021-08-13 03:50:11.573694779 +0000 +++ b2/build.log 2021-08-13 03:57:43.952873469 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 12 15:38:55 -12 2021 -I: pbuilder-time-stamp: 1628825935 +I: Current time: Fri Aug 13 17:50:42 +14 2021 +I: pbuilder-time-stamp: 1628826642 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./prime-phylo_1.0.11-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.MqjNbKte/trustedkeys.kbx': General error -gpgv: Signature made Sun Jul 26 22:24:25 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.6lmoMdCq/trustedkeys.kbx': General error +gpgv: Signature made Tue Jul 28 00:24:25 2020 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ 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/5955/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20609/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/20609/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20609/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,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='8ee2c92c7eee42fa8d5667697d1399ed' - 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='5955' - PS1='# ' - PS2='> ' + INVOCATION_ID=b8d587dd20a94a428257f95dd567ced3 + 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=20609 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/tmp.gnkrahMCme/pbuilderrc_7kJY --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.gnkrahMCme/b1 --logfile b1/build.log prime-phylo_1.0.11-9.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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/tmp.gnkrahMCme/pbuilderrc_mD3W --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.gnkrahMCme/b2 --logfile b2/build.log --extrapackages usrmerge prime-phylo_1.0.11-9.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux virt64b 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 10 21:24 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/5955/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 13 17:50 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 11 23:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/20609/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -341,7 +375,7 @@ Get: 117 http://deb.debian.org/debian bullseye/main armhf liblapack3 armhf 3.9.0-3 [1651 kB] Get: 118 http://deb.debian.org/debian bullseye/main armhf liblapack-dev armhf 3.9.0-3 [1719 kB] Get: 119 http://deb.debian.org/debian bullseye/main armhf libxml2-dev armhf 2.9.10+dfsg-6.7 [722 kB] -Fetched 70.1 MB in 11s (6598 kB/s) +Fetched 70.1 MB in 6s (11.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) @@ -842,8 +876,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (111 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 43949 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. 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_1.0.11-9_source.changes +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_1.0.11-9_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-9 dpkg-buildpackage: info: source distribution unstable @@ -990,7 +1061,7 @@ -- 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 @@ -999,8 +1070,8 @@ make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 -[ 1%] [BISON][MyParser2] Building parser with bison 3.7.5 cd /build/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/flex -o/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c seqreader.l +[ 1%] [BISON][MyParser2] Building parser with bison 3.7.5 cd /build/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c gb.y gb.y: warning: 1 nonterminal useless in grammar [-Wother] gb.y: warning: 1 rule useless in grammar [-Wother] @@ -1014,12 +1085,14 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/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 +[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o +[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o +[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o +[ 3%] 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/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/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 -fdebug-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 -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c -[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /build/prime-phylo-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/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/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 -fdebug-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 -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c -[ 3%] 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/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/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 -fdebug-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 -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 +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/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/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 -fdebug-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 -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 /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] 17 | if (!strcmp(argv[opt], "-d")) { @@ -1033,6 +1106,14 @@ /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; | ^~~~ +/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:1105:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration] + 1105 | 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] seqreader.l: In function 'seq_read': seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable] At top level: @@ -1042,16 +1123,6 @@ /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 ) | ^~~~~~~ -[ 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/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/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 -fdebug-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 -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 -/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:1105:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration] - 1105 | 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] [ 4%] Linking C shared library libprime-phylo-sfile.so cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so CMakeFiles/prime-phylo-sfile.dir/gbread.c.o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -Wl,-rpath,:::::::::::::::::::: @@ -1059,10 +1130,10 @@ [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +[ 4%] [BISON][MyParser] Building parser with bison 3.7.5 [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 -cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c NHX.l -[ 5%] [BISON][MyParser] Building parser with bison 3.7.5 cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c NHXparse.y +cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c NHX.l NHXparse.y:105.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] 105 | %expect 4 | ^~~~~~~ @@ -1073,12 +1144,14 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 5%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c -[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o +[ 7%] 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/NHXnode.c.o +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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:155:25: 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); @@ -1086,8 +1159,12 @@ | | | | int double | %f -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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 ) + | ^~~~~~~ In file included from /usr/include/string.h:495, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c:4: In function 'strncpy', @@ -1095,12 +1172,6 @@ /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 5 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 ) - | ^~~~~~~ [ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/NHXparse.c: In function 'yytree_parse': @@ -1127,6 +1198,8 @@ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; @@ -1236,8 +1309,6 @@ /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 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc [ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: @@ -1248,6 +1319,8 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 423 | catch(std::exception e) | ^ +[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o +cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, 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: @@ -1265,8 +1338,8 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc +[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o +cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, 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: @@ -1281,29 +1354,27 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)': +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc +/usr/include/c++/10/bits/stl_vector.h: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TimeEstimator.cc +/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector beep::option::BeepOptionMap::getDoubleX3(std::string)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc -[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.cc [ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o @@ -1312,6 +1383,8 @@ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /usr/include/c++/10/vector:72, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscTree.hh:6, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscTree.cc:6: @@ -1323,24 +1396,9 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: -/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 300 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 -In file included from /usr/include/c++/10/vector:72, 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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': @@ -1349,9 +1407,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 -/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, 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: @@ -1373,6 +1428,24 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:7, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: +/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 300 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 +/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = beep::Probability; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 +/usr/include/c++/10/bits/vector.tcc:300:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap::set(unsigned int, unsigned int, beep::EpochPtMap::const_iterator) [with T = double]': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:162:14: note: parameter passing for argument of type 'beep::EpochPtMap::const_iterator' {aka 'std::vector >::const_iterator'} changed in GCC 7.1 @@ -1436,6 +1509,8 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:461:14: 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Node.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap::set(unsigned int, unsigned int, beep::EpochPtMap::const_iterator) [with T = beep::Probability]': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:162:14: 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) @@ -1467,6 +1542,10 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:206:14: note: parameter passing for argument of type 'beep::EpochPtMap::const_iterator' {aka 'std::vector >::const_iterator'} changed in GCC 7.1 206 | inline void setWithMax(unsigned i, unsigned j, const_iterator start, const T& upperBound) | ^~~~~~~~~~ +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:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const 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/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap::set(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap::const_iterator) [with T = beep::Probability]': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:403:14: note: parameter passing for argument of type 'beep::EpochPtPtMap::const_iterator' {aka 'std::vector >::const_iterator'} changed in GCC 7.1 403 | inline void set(unsigned i, unsigned j, unsigned p, unsigned q, @@ -1497,14 +1576,6 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:461:14: 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, | ^~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /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:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: @@ -1536,13 +1607,8 @@ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, - 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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, 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: @@ -1577,23 +1643,6 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - 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++/10/bits/stl_vector.h: In member function 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc -[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o -cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc In file included from /usr/include/c++/10/vector:72, 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: @@ -1635,8 +1684,32 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.cc +In file included from /usr/include/c++/10/vector:72, + 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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ [ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:67, + 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++/10/bits/stl_vector.h: In member function 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 960 | _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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 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), @@ -1665,6 +1738,8 @@ /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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc In file included from /usr/include/c++/10/vector:72, 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/BranchSwapping.hh:5, @@ -1674,16 +1749,18 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void beep::OrthologyMCMC::estimateOrthology(bool)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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:118:22: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] 118 | buf[ bytes_read ]=NULL; | ^~~~ -[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc +/usr/include/c++/10/bits/vector.tcc: In member function 'void beep::OrthologyMCMC::estimateOrthology(bool)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc In file included from /usr/include/c++/10/vector:72, 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: @@ -1691,8 +1768,6 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc In file included from /usr/include/c++/10/vector:72, 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: @@ -1704,8 +1779,18 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:22: warning: 'idInt' may be used uninitialized in this function [-Wmaybe-uninitialized] 1049 | new_node = S.addNode(l, r, idInt, name); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /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 Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] + 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc +[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o +cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.cc In file included from /usr/include/c++/10/vector:67, 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: @@ -1713,8 +1798,10 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:67, 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: @@ -1722,22 +1809,12 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc -[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.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 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/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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); @@ -1745,62 +1822,54 @@ /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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc +[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /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$ | ^~ -[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.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 Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] + 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] - 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.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; - | ^~~~~~~~~~~~~~~~~~~~~~ +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. @@ -1809,10 +1878,12 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.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; + | ^~~~~~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/MCMCSampler.cc [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o @@ -1837,6 +1908,8 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/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, @@ -1891,8 +1964,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, from /usr/include/boost/archive/detail/helper_collection.hpp:20, from /usr/include/boost/archive/detail/basic_oarchive.hpp:26, @@ -1907,8 +1980,6 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc /usr/include/c++/10/bits/vector.tcc: In member function 'void beep::MpiMultiGSR::updateGvars(unsigned int)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1919,6 +1990,8 @@ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /usr/include/c++/10/vector:72, 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, @@ -1980,12 +2053,40 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor 'beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: 'beep::EdgeDiscGSR::m_calculatedAtAndBelow' will be initialized after [-Wreorder] + 588 | bool m_calculatedAtAndBelow; + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: 'bool beep::EdgeDiscGSR::m_calculatedAtBars' [-Wreorder] + 583 | bool m_calculatedAtBars; + | ^~~~~~~~~~~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] + 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, + | ^~~~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 475 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable 'xpt' set but not used [-Wunused-but-set-variable] + 485 | Point xpt = x.getPt(); + | ^~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 525 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable 'parent' [-Wunused-variable] + 528 | Node *parent = u->getParent(); + | ^~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable] + 897 | Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first); + | ^~~~~~~~ [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc +[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o +cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /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/libraries/prime/EpochBDTMCMC.cc:1: @@ -2097,36 +2198,22 @@ /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 Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor 'beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: 'beep::EdgeDiscGSR::m_calculatedAtAndBelow' will be initialized after [-Wreorder] - 588 | bool m_calculatedAtAndBelow; - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: 'bool beep::EdgeDiscGSR::m_calculatedAtBars' [-Wreorder] - 583 | bool m_calculatedAtBars; - | ^~~~~~~~~~~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] - 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, - | ^~~~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 475 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable 'xpt' set but not used [-Wunused-but-set-variable] - 485 | Point xpt = x.getPt(); - | ^~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 525 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable 'parent' [-Wunused-variable] - 528 | Node *parent = u->getParent(); - | ^~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable] - 897 | Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first); - | ^~~~~~~~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] + 54 | static const Real MIN_SPLICE_DELTA = 0.0001; + | ^~~~~~~~~~~~~~~~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] + 50 | static const Real REL_TOL = 1e-6; + | ^~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] + 55 | static const Real ABS_TOL = 1e-6; + | ^~~~~~~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc: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:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ @@ -2235,56 +2322,8 @@ /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 Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] - 54 | static const Real MIN_SPLICE_DELTA = 0.0001; - | ^~~~~~~~~~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] - 50 | static const Real REL_TOL = 1e-6; - | ^~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] - 55 | static const Real ABS_TOL = 1e-6; - | ^~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] - 54 | static const Real MIN_SPLICE_DELTA = 0.0001; - | ^~~~~~~~~~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] - 50 | static const Real REL_TOL = 1e-6; - | ^~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] - 55 | static const Real ABS_TOL = 1e-6; - | ^~~~~~~ -In file included from /usr/include/c++/10/vector:72, - 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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - 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++/10/bits/stl_vector.h: In member function 'void beep::EpochBDTProbs::appendInitVals(beep::EpochBDTProbs::realvec&) const': -/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1338 | _M_fill_insert(begin() + __offset, __n, __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ @@ -2394,6 +2433,18 @@ 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] + 54 | static const Real MIN_SPLICE_DELTA = 0.0001; + | ^~~~~~~~~~~~~~~~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] + 50 | static const Real REL_TOL = 1e-6; + | ^~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] + 55 | static const Real ABS_TOL = 1e-6; + | ^~~~~~~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; @@ -2405,6 +2456,26 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ +[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o +cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /usr/include/c++/10/vector:72, + 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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + 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++/10/bits/stl_vector.h: In member function 'void beep::EpochBDTProbs::appendInitVals(beep::EpochBDTProbs::realvec&) const': +/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1338 | _M_fill_insert(begin() + __offset, __n, __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 @@ -2413,6 +2484,10 @@ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.cc +[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o +cd /build/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc In file included from /usr/include/c++/10/vector:72, 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: @@ -2424,10 +2499,8 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.cc -[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -cd /build/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc +[ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o +cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:136:14: warning: variable 'topRateProb' set but not used [-Wunused-but-set-variable] 136 | Probability topRateProb = df->operator()(rate); @@ -2444,8 +2517,6 @@ /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; | ^~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o @@ -2456,52 +2527,52 @@ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.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 Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ +[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o +cd /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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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(); | ^ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o cd /build/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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++/10/vector:72, 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, @@ -2574,6 +2645,8 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc In file included from /usr/include/c++/10/vector:67, from /usr/include/boost/archive/detail/helper_collection.hpp:20, from /usr/include/boost/archive/detail/basic_oarchive.hpp:26, @@ -2599,10 +2672,26 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc +In file included from /usr/include/c++/10/ext/hash_map:60, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: +/usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o +cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 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/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 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++/10/vector:72, 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/LambdaMap.hh:4, @@ -2617,16 +2706,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {beep::GuestTreeModel}; _Tp = beep::GuestTreeModel; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -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 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++/10/ext/hash_map:60, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: -/usr/include/c++/10/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 \ - | ^~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void beep::EnumHybridGuestTreeModel::inits()': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -2634,14 +2713,6 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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 Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ [ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 @@ -2650,13 +2721,17 @@ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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 /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 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const beep::SequenceType&)' has not been declared within 'beep' 270 | ostream& beep::operator<<(ostream& os, const SequenceType& dt) | ^~~~ @@ -2664,6 +2739,10 @@ /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); | ^~~~~~~~ +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 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++) @@ -2671,14 +2750,26 @@ /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/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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc +[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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() + | ^~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:6: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/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: '*.beep::LA_Matrix::dim' is used uninitialized in this function [-Wuninitialized] + 20 | : dim(dim), + | ^~~ In file included from /usr/include/c++/10/map:60, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:2: /usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': @@ -2691,10 +2782,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 -In file included from /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 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++/10/vector:72, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:6: /usr/include/c++/10/bits/vector.tcc: In member function 'std::map beep::SequenceData::getBaseFrequencies()': @@ -2801,22 +2888,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc -[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -cd /build/prime-phylo-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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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: '*.beep::LA_Matrix::dim' is used uninitialized in this function [-Wuninitialized] - 20 | : dim(dim), - | ^~~ [ 81%] Linking CXX shared library libprime-phylo.so cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-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 -pthread -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo.so -o 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CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o CMakeFiles/prime-phylo.dir/SeqIO.cc.o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o CMakeFiles/prime-phylo.dir/SequenceType.cc.o CMakeFiles/prime-phylo.dir/SequenceData.cc.o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -L/usr/lib/arm-linux-gnueabihf/liblapack.so -L/usr/lib/arm-linux-gnueabihf/libblas.so -Wl,-rpath,/usr/lib/arm-linux-gnueabihf/liblapack.so:/usr/lib/arm-linux-gnueabihf/libblas.so:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so /usr/lib/arm-linux-gnueabihf/libboost_mpi.so.1.74.0 /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 @@ -2824,45 +2895,93 @@ [ 81%] Built target prime-phylo make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend -make[3]: Entering directory '/build/prime-phylo-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/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' [ 82%] 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 Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". -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= +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 +[ 83%] 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 Scanning dependencies of target primeDLRS +Scanning dependencies of target primeDTLSR 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 -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -Scanning dependencies of target primeDTLSR 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 make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". -[ 82%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -[ 82%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o +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/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= +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= +[ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc +Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". +Scanning dependencies of target treesize Scanning dependencies of target primeGEM make[3]: Leaving 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 +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' +[ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -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 -fdebug-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 -pthread 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= +Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". +Scanning dependencies of target showtree +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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/EpochPtMaps.hh:9, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ +In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: +/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/applications/primeDLRS/primeDLRS.cc:14: +/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 Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] + 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:13: @@ -2990,84 +3109,41 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: +/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function 'int main(int, char**)': +/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 197 | catch(AnError e) + | ^ +In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] - 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ - | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:14: -/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 Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] - 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: +In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: /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 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/applications/primeGEM/troyo.cc: In function 'int main(int, char**)': -/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 197 | catch(AnError e) +/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:174:37: 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) | ^ -[ 83%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o +[ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/showtree.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.c +[ 87%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -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 -fdebug-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 -pthread 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= -Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". -Scanning dependencies of target treesize -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 -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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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) { - | ^ -[ 85%] 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 -fdebug-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 -pthread 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 -[ 86%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 86%] Built target primeDLRS -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 -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= -Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". -Scanning dependencies of target showtree -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' -[ 87%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc -[ 88%] 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 -fdebug-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 -pthread 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 -[ 89%] 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 -fdebug-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 -pthread 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 +[ 88%] 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 -fdebug-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 -pthread 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' -[ 89%] Built target treesize +[ 88%] 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' -[ 90%] Generating cmdline.c, cmdline.h +[ 89%] 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= Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend.internal". @@ -3076,13 +3152,16 @@ 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' -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o +[ 90%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc -[ 91%] Built target primeDTLSR +[ 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 -fdebug-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 -pthread 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' +[ 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= Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend.internal". @@ -3091,29 +3170,18 @@ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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:174:37: 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -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 -fdebug-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 -pthread 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 -fdebug-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 -pthread 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 +[ 92%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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' -[ 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= Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend.internal". @@ -3122,39 +3190,23 @@ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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) { - | ^ +[ 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 -fdebug-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 -pthread 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 /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] 76 | switch(args_info.input_format_arg) | ^ +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' /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) { | ^ -[ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -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%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc -[ 96%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/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 -fdebug-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 -pthread 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 -[ 97%] 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 -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' -/usr/bin/c++ -g -O2 -fdebug-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 -pthread 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 -[ 97%] 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' -[ 97%] 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= Dependee "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend.internal". @@ -3163,14 +3215,26 @@ 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' -[ 98%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-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 -pthread -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/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) { + | ^ +[ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -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 -fdebug-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 -pthread 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' -[ 98%] Built target reroot -[ 98%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o +[ 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.c +[ 97%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/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"; @@ -3182,6 +3246,11 @@ /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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 98%] 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/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/openmpi -isystem /usr/lib/arm-linux-gnueabihf/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/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 -fdebug-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 -pthread 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) @@ -3197,6 +3266,8 @@ /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) { | ^ +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf' +[ 99%] Built target reroot [ 99%] Linking CXX executable reconcile cd /build/prime-phylo-1.0.11/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-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 -pthread CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/prime-phylo-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 @@ -3215,7 +3286,7 @@ dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -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 @@ -3278,16 +3349,16 @@ 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/primeGEM 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.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' -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/showtree 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: 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/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/reconcile 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.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/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.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' 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 @@ -3296,16 +3367,16 @@ 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: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' -dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/reconcile contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeGEM 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.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' +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: 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/primeDLRS 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.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' -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/primeDTLSR 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 @@ -3319,12 +3390,14 @@ 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/20609/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20609/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/5955 and its subdirectories -I: Current time: Thu Aug 12 15:50:03 -12 2021 -I: pbuilder-time-stamp: 1628826603 +I: removing directory /srv/workspace/pbuilder/20609 and its subdirectories +I: Current time: Fri Aug 13 17:57:39 +14 2021 +I: pbuilder-time-stamp: 1628827059