Diff of the two buildlogs: -- --- b1/build.log 2021-12-08 16:16:51.944948971 +0000 +++ b2/build.log 2021-12-08 16:18:43.577535086 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Dec 8 04:12:10 -12 2021 -I: pbuilder-time-stamp: 1638979930 +I: Current time: Wed Jan 11 12:40:03 +14 2023 +I: pbuilder-time-stamp: 1673390403 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sat Nov 3 19:35:57 2018 -12 +gpgv: Signature made Sun Nov 4 21:35:57 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +31,170 @@ dpkg-source: info: applying 0003-Fix-build-with-Boost-1.67.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2598762/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/52135/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +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/52135/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/52135/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='74ca20c1eadc4c6d8119d54e1500a705' - 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='2598762' - PS1='# ' - PS2='> ' + INVOCATION_ID=45be6fc2f4a347ef9830ba7ffbb8a467 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=52135 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.8jVR8rs7IY/pbuilderrc_DCVj --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.8jVR8rs7IY/b1 --logfile b1/build.log prime-phylo_1.0.11-7.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.8jVR8rs7IY/pbuilderrc_6894 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.8jVR8rs7IY/b2 --logfile b2/build.log prime-phylo_1.0.11-7.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Nov 7 09:58 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/2598762/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jan 11 12:40 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 11 18:20 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/52135/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -335,7 +369,7 @@ Get: 111 http://deb.debian.org/debian buster/main amd64 liblapack-dev amd64 3.8.0-2 [2140 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libxml2-dev amd64 2.9.4+dfsg1-7+deb10u2 [784 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Fetched 73.9 MB in 1s (61.6 MB/s) +Fetched 73.9 MB in 1s (82.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -822,7 +856,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/prime-phylo-1.0.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../prime-phylo_1.0.11-7_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_1.0.11-7_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-7 dpkg-buildpackage: info: source distribution unstable @@ -973,7 +1008,7 @@ -- Build files have been written to: /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/prime-phylo-1.0.11' dh_auto_build -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-1.0.11 -B/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -995,27 +1030,18 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -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/lexer.c.o +[ 3%] 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 -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -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/gb.tab.c.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/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] if (!strcmp(argv[opt], "-d")) { ^~~~~~ -seqreader.l: In function 'seq_read': -seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable] -At top level: -/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: 'input' defined but not used [-Wunused-function] - static int input (void) - ^~~~~ -/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: 'yyunput' defined but not used [-Wunused-function] - static void yyunput (int c, char * yy_bp ) - ^~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_print': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:265:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] printf("%9d", char_counter + 1); @@ -1031,6 +1057,15 @@ 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: +/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: 'input' defined but not used [-Wunused-function] + static int input (void) + ^~~~~ +/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: 'yyunput' defined but not used [-Wunused-function] + static void yyunput (int c, char * yy_bp ) + ^~~~~~~ [ 4%] Linking C shared library libprime-phylo-sfile.so cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -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,:::::::::::::::::::: @@ -1039,8 +1074,8 @@ 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-x86_64-linux-gnu' [ 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-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l [ 5%] [BISON][MyParser] Building parser with bison 3.3.2 +cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l 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-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y NHXparse.y:105.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] %expect 4 @@ -1050,25 +1085,39 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 5%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o +[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o +[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o +[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o +[ 9%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o +[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o +[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o +[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c -[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c -[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c -[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o +[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.cc +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Hacks.cc +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc +[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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/PRNG.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc +[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o +[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.cc +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc /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=] fprintf(stderr, "BW:\t%d\n", l->arg.t); ~^ ~~~~~~~~ %f -[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o -[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.cc -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc +[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c: In function 'yytree_parse': /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:68:25: warning: implicit declaration of function 'yytree_lex'; did you mean 'yytree_parse'? [-Wimplicit-function-declaration] #define yylex yytree_lex @@ -1076,43 +1125,31 @@ /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c:1285:16: note: in expansion of macro 'yylex' yychar = yylex (); ^~~~~ +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc NHXparse.y: In function 'read_tree': NHXparse.y:351:5: warning: implicit declaration of function 'close'; did you mean 'pclose'? [-Wimplicit-function-declaration] NHXparse.y: In function 'read_tree_string': NHXparse.y:399:3: warning: implicit declaration of function 'read_from_string'; did you mean 'read_tree_string'? [-Wimplicit-function-declaration] -[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o NHXparse.y:404:3: warning: implicit declaration of function 'close_string_buffer' [-Wimplicit-function-declaration] -[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16: warning: 'input' defined but not used [-Wunused-function] static int input (void) ^~~~~ -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17: warning: 'yyunput' defined but not used [-Wunused-function] static void yyunput (int c, char * yy_bp ) ^~~~~~~ -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Hacks.cc -[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc -[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.cc cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/DiscTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscTree.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscTree.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::__cxx11::string&, unsigned int, std::vector&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] @@ -1230,8 +1267,6 @@ /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] static const Real D7 = 69997945.0 / 29380423.0; ^~ -[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o @@ -1252,13 +1287,13 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StrStrMap.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc +[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.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] static const Real MIN_SPLICE_DELTA = 0.0001; ^~~~~~~~~~~~~~~~ -[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc [ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeDiscretizer.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: @@ -1277,16 +1312,10 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc -[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 +[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/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:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] - sprAccPropCnt(0, 0) - ^ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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_positive.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1295,6 +1324,12 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.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:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] + sprAccPropCnt(0, 0) + ^ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1306,6 +1341,7 @@ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.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] static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ @@ -1314,7 +1350,6 @@ /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] static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. ^~ -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1330,12 +1365,12 @@ ^~~~~~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc +[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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/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] static const double 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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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] static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. @@ -1346,10 +1381,6 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < t.size(); i++) ~~^~~~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] - static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - ^~ [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1358,12 +1389,16 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] + static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + ^~ +[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCObject.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector*, beep::StrStrMap*, std::map*, std::map*)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:22: warning: 'idInt' may be used uninitialized in this function [-Wmaybe-uninitialized] new_node = S.addNode(l, r, idInt, name); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o @@ -1378,6 +1413,14 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleObserver.cc +[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc +[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.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] + 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/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] static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. @@ -1386,22 +1429,14 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/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] - static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - ^~~ -[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc -[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc -[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc -[ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.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] unsigned check_number_nonupdate = 0; ^~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o +[ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.cc [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1414,22 +1449,22 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function 'virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point] - p[++i] = geneFams[i]->initStateProb();//updateDataProbability(); - ^~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point] -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point] [ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 -[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc +[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function 'virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point] + p[++i] = geneFams[i]->initStateProb();//updateDataProbability(); + ^~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point] +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:338:6: warning: operation on 'i' may be undefined [-Wsequence-point] 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: @@ -1541,6 +1576,8 @@ /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] static const Real D7 = 69997945.0 / 29380423.0; ^~ +[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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: /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] @@ -1651,28 +1688,12 @@ /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] static const Real D7 = 69997945.0 / 29380423.0; ^~ -[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc -[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc 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] static const Real MIN_SPLICE_DELTA = 0.0001; ^~~~~~~~~~~~~~~~ -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] - static const Real MIN_SPLICE_DELTA = 0.0001; - ^~~~~~~~~~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: -/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] - 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] - static const Real ABS_TOL = 1e-6; - ^~~~~~~ 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] @@ -1681,6 +1702,8 @@ /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] static const Real ABS_TOL = 1e-6; ^~~~~~~ +[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.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] @@ -1837,6 +1860,18 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc +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] + static const Real MIN_SPLICE_DELTA = 0.0001; + ^~~~~~~~~~~~~~~~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: +/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] + 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] + static const Real ABS_TOL = 1e-6; + ^~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1849,6 +1884,8 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc +[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.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] Probability topRateProb = df->operator()(rate); @@ -1865,20 +1902,18 @@ /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] Real zeroTotalQuotient = 0.0; ^~~~~~~~~~~~~~~~~ -[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.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] 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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1889,10 +1924,6 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::__cxx11::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] - typedef std::map::const_iterator MapIter; - ^~~~~~~ [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1911,38 +1942,38 @@ cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.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] - ReconciliationTreeGenerator:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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] +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::__cxx11::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] typedef std::map::const_iterator MapIter; ^~~~~~~ [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.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] + typedef std::map::const_iterator MapIter; + ^~~~~~~ +/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] + ReconciliationTreeGenerator:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.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:367:43: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] + if(rootNode && bTree.getRootNode() == false) + ^~~~~ [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.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:367:43: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] - if(rootNode && bTree.getRootNode() == false) - ^~~~~ [ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc [ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] - static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - ^~ [ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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 @@ -1961,29 +1992,29 @@ ^~~~~~~ [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/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] - 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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] + static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + ^~ +[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/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] + 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] static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. ^~~ -[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.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] static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. ^~~ -[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const beep::SequenceType&)' has not been declared within 'beep' ostream& beep::operator<<(ostream& os, const SequenceType& dt) ^~~~ @@ -1991,6 +2022,16 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a 'friend' friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); ^~~~~~~~ +[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -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-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + ^~~ /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] LA_Matrix::LA_Matrix() @@ -1999,12 +2040,6 @@ /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] : dim(dim), ^~~ -[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 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] for (int i = 0; i < seqType.alphabetSize(); i++) @@ -2018,112 +2053,113 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 81%] Built target prime-phylo make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend +make -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 -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-x86_64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= -make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color= -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-x86_64-linux-gnu' -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-x86_64-linux-gnu' make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend -[ 82%] Generating cmdline.c, cmdline.h -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend -Scanning dependencies of target primeDTLSR -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build -[ 83%] Generating cmdline.c, cmdline.h make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 81%] Generating cmdline.c, cmdline.h +[ 82%] Generating cmdline.c, cmdline.h [ 83%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h -Scanning dependencies of target primeDLRS -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 85%] Generating cmdline.c, cmdline.h -make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 85%] Generating cmdline.c, cmdline.h -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= [ 85%] Generating cmdline.c, cmdline.h -[ 85%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc +[ 85%] Generating cmdline.c, cmdline.h +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames +Scanning dependencies of target primeDLRS +Scanning dependencies of target primeDTLSR +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake --color= -[ 85%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -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-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake --color= -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color= +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake --color= -Scanning dependencies of target primeGEM -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color= -Scanning dependencies of target reconcile -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake --color= +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color= +[ 85%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc +[ 85%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc Scanning dependencies of target treesize -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' Scanning dependencies of target showtree -make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +Scanning dependencies of target primeGEM Scanning dependencies of target reroot -[ 85%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +Scanning dependencies of target reconcile +Scanning dependencies of target tree2leafnames make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build -Scanning dependencies of target chainsaw +make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -Scanning dependencies of target tree2leafnames -make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build +Scanning dependencies of target chainsaw make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 86%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -[ 86%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime 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-I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c -[ 87%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime 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src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o +[ 86%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o +[ 87%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o +[ 88%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong 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CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.c -[ 90%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc 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-I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile/cmdline.c +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot/cmdline.c +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc +[ 91%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o +[ 92%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/treesize.dir/treesize.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/showtree.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c -[ 92%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc -[ 93%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c +[ 93%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c +[ 94%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.c: In function 'update_arg': /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.c:395:9: warning: variable 'stop_char' set but not used [-Wunused-but-set-variable] char *stop_char = 0; @@ -2132,12 +2168,7 @@ /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/cmdline.c:483:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable] int check_required; ^~~~~~~~~~~~~~ -/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c: In function 'cmdline_parser_internal': -/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c:554:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable] - int check_required; - ^~~~~~~~~~~~~~ -[ 94%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -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/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c: In function 'update_arg': /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c:388:9: warning: variable 'stop_char' set but not used [-Wunused-but-set-variable] char *stop_char = 0; @@ -2146,26 +2177,16 @@ /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c:472:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable] int check_required; ^~~~~~~~~~~~~~ +/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c: In function 'cmdline_parser_internal': +/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree/cmdline.c:554:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable] + int check_required; + ^~~~~~~~~~~~~~ [ 94%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c: In function 'cmdline_parser_internal': /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c:539:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable] int check_required; ^~~~~~~~~~~~~~ -/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] - 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=] - catch (AnError e) { - ^ -/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)': -/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] - 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=] - 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] bool et, nt, bl, nw; @@ -2177,20 +2198,35 @@ /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=] catch (AnError e) ^ -[ 95%] Linking CXX executable treesize -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so +/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] + 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=] + catch (AnError e) { + ^ +/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] + 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=] + catch (AnError e) { + ^ +[ 95%] Linking CXX executable showtree +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so [ 95%] Linking CXX executable tree2leafnames cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so -[ 96%] Linking CXX executable showtree -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 96%] Built target treesize +[ 96%] Linking CXX executable treesize +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 96%] Built target showtree make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 96%] Built target tree2leafnames +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 96%] Built target treesize /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] char *ofilename = "mpr.out"; @@ -2198,7 +2234,6 @@ /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] catch (AnError e) { ^ -[ 96%] Built target tree2leafnames /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < gtree.getNumberOfNodes(); i++) { @@ -2209,6 +2244,10 @@ /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] static const Real MIN_SPLICE_DELTA = 0.0001; ^~~~~~~~~~~~~~~~ +/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=] + catch(AnError e) + ^ 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: @@ -2336,6 +2375,10 @@ /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] 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/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] + static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + ^~~ /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] switch(ai.guest_tree_format_arg) @@ -2351,14 +2394,6 @@ /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=] catch (AnError e) { ^ -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] - 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=] - catch(AnError e) - ^ 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] static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ @@ -2381,27 +2416,27 @@ [ 96%] Linking CXX executable reconcile cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/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-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so +[ 96%] Linking CXX executable primeGEM +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 96%] Built target reconcile [ 97%] Linking CXX executable chainsaw cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so -[ 97%] Linking CXX executable primeGEM -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 97%] Built target chainsaw make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 97%] Built target primeGEM +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 97%] Built target chainsaw [ 98%] Linking CXX executable reroot cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 98%] Built target reroot [ 99%] Linking CXX executable primeDTLSR cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 99%] Built target reroot -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' [ 99%] Built target primeDTLSR [100%] Linking CXX executable primeDLRS cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1 @@ -2418,7 +2453,7 @@ dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/prime-phylo-1.0.11/debian/prime-phylo AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/prime-phylo-1.0.11 -B/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -2444,18 +2479,18 @@ [ 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-x86_64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend 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-x86_64-linux-gnu' +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= 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-x86_64-linux-gnu' +cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' cd /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= @@ -2472,55 +2507,55 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build +make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/cxx/tools/showtree/CMakeFiles/showtree.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 83%] Built target showtree make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build'. +make[3]: Nothing to be done for 'src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 86%] Built target reconcile -[ 88%] Built target primeGEM make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/cxx/tools/treesize/CMakeFiles/treesize.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 91%] Built target treesize -[ 93%] Built target tree2leafnames make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build'. +make[3]: Nothing to be done for 'src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/cxx/tools/reroot/CMakeFiles/reroot.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' -[ 95%] Built target chainsaw -[ 98%] Built target reroot +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +make[3]: Nothing to be done for 'src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build'. +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 83%] Built target showtree make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build'. make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' +[ 86%] Built target reconcile +[ 88%] Built target tree2leafnames +[ 91%] Built target reroot +[ 94%] Built target treesize +[ 96%] Built target primeGEM +[ 98%] Built target chainsaw [ 99%] Built target primeDTLSR [100%] Built target primeDLRS make[2]: Leaving directory '/build/prime-phylo-1.0.11/obj-x86_64-linux-gnu' @@ -2590,8 +2625,6 @@ dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' @@ -2610,6 +2643,8 @@ dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' @@ -2624,8 +2659,8 @@ dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-7_amd64.deb'. dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-7_amd64.deb'. +dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-7_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../prime-phylo_1.0.11-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2633,12 +2668,14 @@ 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/52135/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/52135/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/2598762 and its subdirectories -I: Current time: Wed Dec 8 04:16:51 -12 2021 -I: pbuilder-time-stamp: 1638980211 +I: removing directory /srv/workspace/pbuilder/52135 and its subdirectories +I: Current time: Wed Jan 11 12:41:53 +14 2023 +I: pbuilder-time-stamp: 1673390513